Re: [Bioc-devel] Windows build error

[Jennifer Wokaty]

Hi,

cfTools will be still be included in 3.17. I don't see the error relating to 
conda on today's build report. We don't directly manage conda on the builders 
and allow basilisk to handle it. I can try clearing the cache on the 3.17 
Windows builder this week to see if that helps.

Jennifer Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team

From: Bioc-devel  on behalf of RAN HU 

Sent: Thursday, April 20, 2023 2:58 PM
To: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Windows build error

***ATTENTION: This email came from an external source. Do not open attachments 
or click on links from unknown senders or unexpected emails.***


Dear BioC team,

I wonder if this error is caused by your Windows environment. Or is there
anything I can do to fix it?

If this Windows build error is not solved, will cfTools still be included
in the 3.17 release version?

Thanks in advance!

Best,
Ran

On Tue, Apr 18, 2023 at 4:46 PM RAN HU  wrote:

> Hi all,
>
> My package cfTools has recently been accepted. I just found that there is
> a build error on Windows: Multiple platform build/check report for BioC
> 3.17 - BUILD results for cfTools on palomino3 (bioconductor.org)
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.17_bioc-2DLATEST_cfTools_palomino3-2Dbuildsrc.html=DwIFaQ=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA=a5vg0H-TJG4KeZppnKMuNeJ5EAUERiCoGcYn3fd9i4oH62Nu-WzHwN2s1gQRetTh=KOoT4OpK2XZLs9HelMrfHFQOnn7jiUQUwZZVoZ4tUPE=
>  >,
> citing:
>
> ==> WARNING: A newer version of conda exists. <==
>   current version: 4.12.0
>   latest version: 23.3.1
>
> Please update conda by running
>
> $ conda update -n base -c defaults conda
>
> Quitting from lines 160-162 (cfTools-vignette.Rmd)
> Error: processing vignette 'cfTools-vignette.Rmd' failed with diagnostics:
> cannot open the connection
> --- failed re-building 'cfTools-vignette.Rmd'
>
> How can I fix this?
>
> Many thanks,
> Ran
>

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Re: [Bioc-devel] Windows build error

[RAN HU]

Dear BioC team,

I wonder if this error is caused by your Windows environment. Or is there
anything I can do to fix it?

If this Windows build error is not solved, will cfTools still be included
in the 3.17 release version?

Thanks in advance!

Best,
Ran

On Tue, Apr 18, 2023 at 4:46 PM RAN HU  wrote:

> Hi all,
>
> My package cfTools has recently been accepted. I just found that there is
> a build error on Windows: Multiple platform build/check report for BioC
> 3.17 - BUILD results for cfTools on palomino3 (bioconductor.org)
> ,
> citing:
>
> ==> WARNING: A newer version of conda exists. <==
>   current version: 4.12.0
>   latest version: 23.3.1
>
> Please update conda by running
>
> $ conda update -n base -c defaults conda
>
> Quitting from lines 160-162 (cfTools-vignette.Rmd)
> Error: processing vignette 'cfTools-vignette.Rmd' failed with diagnostics:
> cannot open the connection
> --- failed re-building 'cfTools-vignette.Rmd'
>
> How can I fix this?
>
> Many thanks,
> Ran
>

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[Bioc-devel] Windows build error

[RAN HU]

Hi all,

My package cfTools has recently been accepted. I just found that there is a
build error on Windows: Multiple platform build/check report for BioC 3.17
- BUILD results for cfTools on palomino3 (bioconductor.org)
,
citing:

==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.3.1

Please update conda by running

$ conda update -n base -c defaults conda

Quitting from lines 160-162 (cfTools-vignette.Rmd)
Error: processing vignette 'cfTools-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'cfTools-vignette.Rmd'

How can I fix this?

Many thanks,
Ran

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Re: [Bioc-devel] Windows specific error during CHECK

[Hervé Pagès]

Hi Felix,

Interestingly the unit tests error on 64-bit Windows is gone today but 
now the unit tests trigger a segfault on Linux:



https://bioconductor.org/checkResults/3.14/bioc-LATEST/mia/nebbiolo2-checksrc.html

The segfault seems to happen during a call to ape:::all.equal.phylo(). 
This kind of hard-to-reproduce segfault is usually caused by some 
problematic native code. The usual suspects are uninitialized C 
variables/arrays. Running the problematic test thru Valgrind might give 
you some hints.


Best,
H.


On 26/10/2021 13:09, Felix Ernst wrote:

Thanks Herve!

-Ursprüngliche Nachricht-
Von: Hervé Pagès 
Gesendet: Dienstag, 26. Oktober 2021 21:53
An: Felix Ernst ; bioc-devel@r-project.org
Betreff: Re: [Bioc-devel] Windows specific error during CHECK

Hi Felix,

On 26/10/2021 12:10, Felix Ernst wrote:

Hi Bioc-Team,

I have got a problem with an error on Windows, which I am not able to debug.

http://bioconductor.org/checkResults/devel/bioc-LATEST/mia/riesling1-c
hecksrc.html

The testthat.out.fail output doesn't indicate any problems and the testthat.out 
on other systems looks the same.

Can someone provide any hint on what might be going on? Thanks in advance!


Hmm.. even more puzzling is that if I go on riesling1, start R (in 64-bit 
mode), and run the tests manually, I don't see any problem:

  > test_check("mia")

  
|==|

100%



Time difference of 6.58 secs



Initializing error rates to maximum possible estimate.

selfConsist step 1 .

 selfConsist step 2

 selfConsist step 3

 selfConsist step 4

Convergence after  4  rounds.

Initializing error rates to maximum possible estimate.

selfConsist step 1 .

 selfConsist step 2

 selfConsist step 3

 selfConsist step 4

Convergence after  4  rounds.

initial  value 0.383462

iter   5 value 0.161655

iter  10 value 0.113278

final  value 0.003270

converged

initial  value 0.00

final  value 0.00

converged

initial  value 0.00

final  value 0.00

converged

initial  value 0.00

final  value 0.00

converged

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 630 ]


So this only seems to happen in the context of 'R CMD check'. I wonder
if the fact that we run 'R CMD check' with the --force-multiarch option
(so the examples and tests are run for the 2 Windows archs) could be
somehow related to the issue.

Anyways, I won't be able to do more testing today because the builds on
riesling1 are going to start in a few minutes. I'll try to get back to
this tomorrow.

Cheers,
H.




Best regards,
Felix

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Bioconductor Core Team
hpages.on.git...@gmail.com

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Re: [Bioc-devel] Windows specific error during CHECK

[Felix Ernst]

Thanks Herve!

-Ursprüngliche Nachricht-
Von: Hervé Pagès  
Gesendet: Dienstag, 26. Oktober 2021 21:53
An: Felix Ernst ; bioc-devel@r-project.org
Betreff: Re: [Bioc-devel] Windows specific error during CHECK

Hi Felix,

On 26/10/2021 12:10, Felix Ernst wrote:
> Hi Bioc-Team,
> 
> I have got a problem with an error on Windows, which I am not able to debug.
> 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/mia/riesling1-c
> hecksrc.html
> 
> The testthat.out.fail output doesn't indicate any problems and the 
> testthat.out on other systems looks the same.
> 
> Can someone provide any hint on what might be going on? Thanks in advance!

Hmm.. even more puzzling is that if I go on riesling1, start R (in 64-bit 
mode), and run the tests manually, I don't see any problem:

 > test_check("mia")

 
|==|
100%



Time difference of 6.58 secs



Initializing error rates to maximum possible estimate.

selfConsist step 1 .

selfConsist step 2

selfConsist step 3

selfConsist step 4

Convergence after  4  rounds.

Initializing error rates to maximum possible estimate.

selfConsist step 1 .

selfConsist step 2

selfConsist step 3

selfConsist step 4

Convergence after  4  rounds.

initial  value 0.383462

iter   5 value 0.161655

iter  10 value 0.113278

final  value 0.003270

converged

initial  value 0.00

final  value 0.00

converged

initial  value 0.00

final  value 0.00

converged

initial  value 0.00

final  value 0.00

converged

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 630 ]


So this only seems to happen in the context of 'R CMD check'. I wonder 
if the fact that we run 'R CMD check' with the --force-multiarch option 
(so the examples and tests are run for the 2 Windows archs) could be 
somehow related to the issue.

Anyways, I won't be able to do more testing today because the builds on 
riesling1 are going to start in a few minutes. I'll try to get back to 
this tomorrow.

Cheers,
H.


> 
> Best regards,
> Felix
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> 

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Re: [Bioc-devel] Windows specific error during CHECK

[Hervé Pagès]

Hi Felix,

On 26/10/2021 12:10, Felix Ernst wrote:

Hi Bioc-Team,

I have got a problem with an error on Windows, which I am not able to debug.

http://bioconductor.org/checkResults/devel/bioc-LATEST/mia/riesling1-checksrc.html

The testthat.out.fail output doesn't indicate any problems and the testthat.out 
on other systems looks the same.

Can someone provide any hint on what might be going on? Thanks in advance!


Hmm.. even more puzzling is that if I go on riesling1, start R (in 
64-bit mode), and run the tests manually, I don't see any problem:


> test_check("mia")


|==| 
100%




Time difference of 6.58 secs



Initializing error rates to maximum possible estimate.

selfConsist step 1 .

   selfConsist step 2

   selfConsist step 3

   selfConsist step 4

Convergence after  4  rounds.

Initializing error rates to maximum possible estimate.

selfConsist step 1 .

   selfConsist step 2

   selfConsist step 3

   selfConsist step 4

Convergence after  4  rounds.

initial  value 0.383462

iter   5 value 0.161655

iter  10 value 0.113278

final  value 0.003270

converged

initial  value 0.00

final  value 0.00

converged

initial  value 0.00

final  value 0.00

converged

initial  value 0.00

final  value 0.00

converged

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 630 ]


So this only seems to happen in the context of 'R CMD check'. I wonder 
if the fact that we run 'R CMD check' with the --force-multiarch option 
(so the examples and tests are run for the 2 Windows archs) could be 
somehow related to the issue.


Anyways, I won't be able to do more testing today because the builds on 
riesling1 are going to start in a few minutes. I'll try to get back to 
this tomorrow.


Cheers,
H.




Best regards,
Felix

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hpages.on.git...@gmail.com

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[Bioc-devel] Windows specific error during CHECK

[Felix Ernst]

Hi Bioc-Team,

I have got a problem with an error on Windows, which I am not able to debug.

http://bioconductor.org/checkResults/devel/bioc-LATEST/mia/riesling1-checksrc.html

The testthat.out.fail output doesn't indicate any problems and the testthat.out 
on other systems looks the same.

Can someone provide any hint on what might be going on? Thanks in advance!

Best regards,
Felix

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Re: [Bioc-devel] Windows-specific Function Not Found Error

[Dario Strbenac via Bioc-devel]

Hello,

Ah, I had a few different uses of MultiAssayExperiment::colData in a particular 
function of the package, but one line had only colData without the scoping in 
front. I wish that R error messages displayed R file names and line numbers 
more often.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] Windows-specific Function Not Found Error

[Martin Morgan]

Remember that Windows doesn�t have �forked� parallelism; all processes are 
running in separate processes where the functions in use need to be made 
explicitly available.

Likely you can emulate this error on non-windows by using �SnowParam()� instead 
of MulticoreParam(), e.g.,

> library(SummarizedExperiment)
> library(BiocParallel)
> result <- bplapply(1:2, function(i) colData, BPPARAM = MulticoreParam(2))
> result <- bplapply(1:2, function(i) colData, BPPARAM = SnowParam(2))
Error: BiocParallel errors
  2 remote errors, element index: 1, 2
  0 unevaluated and other errors
  first remote error: object 'colData' not found

Solve the problem by explicitly indicating the source of the function

> result <- bplapply(1:2, function(i) SummarizedExperiment::colData, BPPARAM = 
> SnowParam(2))

or perhaps something along the lines of

FUN = function(i) {
library(SummarizedExperiment)
   colData
}

I would guess that your package Depends: but does not Import the package where 
colData is defined; I think BiocParallel would normally serialize the package 
environment, and hence colData, to the worker�

Martin

On 10/12/21, 7:00 PM, "Bioc-devel"  wrote:
Good day,

I see a checking failure for ClassifyR for Windows Server 2019 only. The error 
is

Error: BiocParallel errors
  4 remote errors, element index: 1, 4, 6, 8
  6 unevaluated and other errors
  first remote error: could not find function "colData"

Is there anything I can change in my code to help it pass? The error doesn't 
appear on the two other Bioconductor  servers.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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[Bioc-devel] Windows-specific Function Not Found Error

[Dario Strbenac via Bioc-devel]

Good day,

I see a checking failure for ClassifyR for Windows Server 2019 only. The error 
is

Error: BiocParallel errors
  4 remote errors, element index: 1, 4, 6, 8
  6 unevaluated and other errors
  first remote error: could not find function "colData"

Is there anything I can change in my code to help it pass? The error doesn't 
appear on the two other Bioconductor  servers.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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[Bioc-devel] Windows Not Connected to Internet?

[Margaret Linan]

 Hi -

I recently updated the PoTRA release 3_13, but see that the same error is
showing up.

##
##
###
### Running command:
###
###   chmod a+r PoTRA -R &&
C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD build
--keep-empty-dirs --no-resave-data PoTRA
###
##
##


* checking for file 'PoTRA/DESCRIPTION' ... OK
* preparing 'PoTRA':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'PoTRA.Rmd' using rmarkdown
Quitting from lines 223-227 (PoTRA.Rmd) Error: processing vignette
'PoTRA.Rmd' failed with diagnostics:
cannot download pathway data: are you offline?
--- failed re-building 'PoTRA.Rmd'

SUMMARY: processing the following file failed:
  'PoTRA.Rmd'

Error: Vignette re-building failed.
Execution halted

This vignette code works in the Linux and Mac builds and these builds are
100% successful so I am wondering why it doesn't succeed in the Windows
build.


Thanks
Margaret

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Re: [Bioc-devel] Windows build. error: "DLL 'RcppParallel' not found: maybe not installed for this architecture?"

[Kern, Lori]

A new version of RcppParallel was pushed to CRAN yesterday. The builders should 
pick this up automatically and we hope it should resolve in the next day or 
two. If it does not we will follow up.

Thank you for the report.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of stefano 

Sent: Wednesday, May 5, 2021 8:55 PM
To: bioc-devel 
Subject: [Bioc-devel] Windows build. error: "DLL 'RcppParallel' not found: 
maybe not installed for this architecture?"

Hello,

the package ppcseq fails on windows build (Multiple platform build/check
report for BioC 3.13 - INSTALL report for ppcseq on riesling1
(bioconductor.org)
<https://secure-web.cisco.com/1WIggmfKSOnQ7fWX0pJXyIWrLJCQYfUMqFIB3TwJX8Nc5iH4ewyCzsJRSq_zASwIKy5Sn6wDwwHWtEp3u0bOpC2y9Ugnplhwss1q0MDNXTXHHorUGIZzrQYEGSuK5-anXPorUbqJTOaD2djXKdP7Uv1Oq9OEX5E8YjN1GgnssQR5dw3L7y5xyxjcN_WT4TZmKYnH484jrcxBCoZ9UBQ1V9mPaftNFXcXM3BCU3rUN2wFRHR794gV188oXy0YBSA7b3UW6dXQJ4tSpX6DSbNNQgcNCA9hKOGtko-6gt24l-dw4aNQ_MuU-hsEYalgbwQhT/https%3A%2F%2Fwww.bioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2Fppcseq%2Friesling1-install.html>)
because of the lack of RcppParallel in the windows build.

Any chance this can be fixed?

Thanks a lot.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544

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[Bioc-devel] Windows build. error: "DLL 'RcppParallel' not found: maybe not installed for this architecture?"

[stefano]

Hello,

the package ppcseq fails on windows build (Multiple platform build/check
report for BioC 3.13 - INSTALL report for ppcseq on riesling1
(bioconductor.org)
)
because of the lack of RcppParallel in the windows build.

Any chance this can be fixed?

Thanks a lot.

Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544

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[Bioc-devel] Windows build warnings from basilisk configure file

[Zhang, David]

Hi,

I have submitted the package dasper as an additional package to megadepth to 
Bioconductor 3.12: https://github.com/Bioconductor/Contributions/issues/1696

dasper interfaces into python using the Bioconductor package basilisk. I’ve 
included a configure file in the root of the dasper package following the 
set-up instructions of the basilisk package. However, this causes a build 
report warning on Windows:

Warning: file 'dasper/configure' did not have execute permissions: corrected

When checking, the configure file does have both read + execute permissions. I 
was wondering if this is a known build issue or if you had an idea how to 
resolve this warning?

Build report: 
http://bioconductor.org/spb_reports/dasper_buildreport_20201019202946.html
Associated comment: 
https://github.com/Bioconductor/Contributions/issues/1696#issuecomment-712926157

Thanks in advance,

David

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Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

We currently do not have a devel devel Mac builder so this is true for all 
packages.  We are working on a replacement.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Charles Warden 
Sent: Monday, May 4, 2020 12:04 PM
To: Herv�� Pag��s ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi Everybody,

It looks like the error is now fixed (from changing the Perl code) in the 
release and devel versions:

https://secure-web.cisco.com/1rwACYNhrzVovETfJlqiLYgx4VYKabnfwXimhOWWMwCxnQDtrwantaRsPH_X_f6kyTeNPzVs9BWzaYvKyE1J32IOvPpDPFBtvUPeakl35MuvJDbMyxHdEk3KEuM2ohLE6Dzy7zwNrgAW7tv6pN2SfzkzYIKIHyj6NsIAC85s82ys71aY6M3qoXkRe42IOaPrMOaDKbQHFvZRIXsve00bbpILuLb2aDsCwFu4nc-h0baKL3wAavkmzKuR3ylG9d-iy6Xd8Fa-YjHzKEfnb7zb0kXE0krD49l5_J3jamvI9BlD73WRb-jSN3j2p8o_9czY3dqRiZOLxO7slZfC0ADwAMA/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FCOHCAP.html

https://secure-web.cisco.com/1U_Wn1Yz4M7uaaynffS2E0dB0mGlhnf4RGqc7NrlPm299KzGFANDAGbdG5kdorSM1zErIoFN9yDkKK4oPSMvA9mEuf86uDmFYyoMfBHHGXWI4CEMYCDQw8b4mMYRmwimYsFqtqXw4Xol5YXp0IfewFP5WQSmpDv9Zf1Bvw2eomILm9jGKZ-FIR2t8mQwbSz9-wxaYtWvwWBlYF0RspD81jqkxuM45ZRPJXJk4h5k7XChQiVzgg60EsG-sf4ehk8x7yrDfA-CBJT6V3PIn6y_pdeu98Yinj4uJ_xNKR6v3S-lhNQWzo_NZBDcKXVbVEYVVEh09hlp9H92O0U7TMYRNNQ/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FCOHCAP.html

I noticed there wasn't a Mac test for the devel version, but perhaps that is 
true for all packages?

Thank you very much for your help!

Sincerely,
Charles

-Original Message-
From: Herv�� Pag��s 
Sent: Tuesday, April 28, 2020 10:55 AM
To: Charles Warden ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

It is not clear what the purpose of these "if" statement is. Apparently to set 
the $os_name variable but then where is this variable used and for what?

So you might want to revisit the need for these tests. Maybe you don't need 
them after all.

Another problem is that the temporary files generated by your Perl scripts are 
generated in the current working directory. As discussed earlier, this is not 
good. Please make sure that all temporary files are generated in tempdir().

Thanks!
H.


On 4/28/20 10:43, Charles Warden wrote:
> Hi H,
>
> Thank you for pointing that out.
>
> I am currently not seeing errors on my Windows computer, but I see that I 
> need to add "msys" for Windows on your system (and add quotes as well as make 
> the error message more clear).  I have a 64-bit Windows computer and I didn't 
> get an error message, but I can see how this could cause problems.  I 
> apologize for not realizing that.
>
> It sounds like I should wait a little while to do that.  However, I think 
> this does sound correct, and I will make that change.
>
> Thank You,
> Charles
>
> -Original Message-
> From: Herv�� Pag��s 
> Sent: Tuesday, April 28, 2020 10:32 AM
> To: Charles Warden ; Shepherd, Lori
> ; 'bioc-devel@r-project.org'
> 
> Subject: Re: [Bioc-devel] Windows Development Build Error Message for
> COHCAP
>
> Hi Charles,
>
> The error you get on Windows is because your Perl script integrate_island.pl 
> fails on this platform. It contains the following code:
>
> if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
>   {
>   #Mac
>   $os_name = "MAC";
>   }#end if ($os eq "MacOS")
> elsif ($os eq "MSWin32")
>   {
>   #PC
>   $os_name = "PC";
>   }#end if ($os eq "MacOS")
> else
>   {
>   print "Need to specify folder structure for $os!\n";
>   exit;
>   }#end else
>
> The major problem with this code is that the script will exit
> **normally** without doing anything if the detected OS is not one of the 
> expected ones. So the 'temp_paired_367853.txt' file is not produced and your 
> R code later fails to open it (when you try to read the file with 
> read.table()).
>
> Note that before exiting, your Perl script displays:
>
> Need to specify folder structure for msys!
>
> which you can see in the report. This gives you a BIG clue of what the 
> problem is and how to fix it.
>
> If you develop your package on Windows (and it seems you do), the
> problem should be very reproducible for you, granted that you use R
> 4.0.0 for that of course.
>
> Thanks,
> H.
>
>
> On 4/28/20 09:02, Charles Warden

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Charles Warden]

Hi Everybody,

It looks like the error is now fixed (from changing the Perl code) in the 
release and devel versions:

https://www.bioconductor.org/packages/release/bioc/html/COHCAP.html

https://www.bioconductor.org/packages/devel/bioc/html/COHCAP.html

I noticed there wasn't a Mac test for the devel version, but perhaps that is 
true for all packages?

Thank you very much for your help!

Sincerely,
Charles

-Original Message-
From: Hervé Pagès  
Sent: Tuesday, April 28, 2020 10:55 AM
To: Charles Warden ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

It is not clear what the purpose of these "if" statement is. Apparently to set 
the $os_name variable but then where is this variable used and for what?

So you might want to revisit the need for these tests. Maybe you don't need 
them after all.

Another problem is that the temporary files generated by your Perl scripts are 
generated in the current working directory. As discussed earlier, this is not 
good. Please make sure that all temporary files are generated in tempdir().

Thanks!
H.


On 4/28/20 10:43, Charles Warden wrote:
> Hi H,
> 
> Thank you for pointing that out.
> 
> I am currently not seeing errors on my Windows computer, but I see that I 
> need to add "msys" for Windows on your system (and add quotes as well as make 
> the error message more clear).  I have a 64-bit Windows computer and I didn't 
> get an error message, but I can see how this could cause problems.  I 
> apologize for not realizing that.
> 
> It sounds like I should wait a little while to do that.  However, I think 
> this does sound correct, and I will make that change.
> 
> Thank You,
> Charles
> 
> -Original Message-
> From: Hervé Pagès 
> Sent: Tuesday, April 28, 2020 10:32 AM
> To: Charles Warden ; Shepherd, Lori 
> ; 'bioc-devel@r-project.org' 
> 
> Subject: Re: [Bioc-devel] Windows Development Build Error Message for 
> COHCAP
> 
> Hi Charles,
> 
> The error you get on Windows is because your Perl script integrate_island.pl 
> fails on this platform. It contains the following code:
> 
> if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
>   {
>   #Mac
>   $os_name = "MAC";
>   }#end if ($os eq "MacOS")
> elsif ($os eq "MSWin32")
>   {
>   #PC
>   $os_name = "PC";
>   }#end if ($os eq "MacOS")
> else
>   {
>   print "Need to specify folder structure for $os!\n";
>   exit;
>   }#end else
> 
> The major problem with this code is that the script will exit
> **normally** without doing anything if the detected OS is not one of the 
> expected ones. So the 'temp_paired_367853.txt' file is not produced and your 
> R code later fails to open it (when you try to read the file with 
> read.table()).
> 
> Note that before exiting, your Perl script displays:
> 
> Need to specify folder structure for msys!
> 
> which you can see in the report. This gives you a BIG clue of what the 
> problem is and how to fix it.
> 
> If you develop your package on Windows (and it seems you do), the 
> problem should be very reproducible for you, granted that you use R
> 4.0.0 for that of course.
> 
> Thanks,
> H.
> 
> 
> On 4/28/20 09:02, Charles Warden wrote:
>> Hi Lori,
>>
>> Thank you very much.
>>
>> I was thinking about reverting the change to test not specifying the 
>> full file path at one point (in *v1.33.6*), but I was planning on 
>> keeping the change to using a temporary directory in *v1.33.4*.
>> Essentially, I tested making that change in *v1.33.6* because there 
>> was still an error message in *v1.33.4.*
>>
>> However, I will wait to see what else you suggest, before making any 
>> additional changes.  From my end, there is no need to rush, and I can 
>> wait until next week (or later).
>>
>> You probably already know this, but it looks like *v1.33.6 *is in the 
>> release version without any errors (although it does look like the 
>> Windows version is different):
>>
>> https://urldefense.com/v3/__https://www.bioconductor.org/packages/rel
>> e 
>> ase/bioc/html/COHCAP.html__;!!Fou38LsQmgU!_wdP4PPRbzvocGetxQ4gXCipwd4
>> _
>> 1cOH4l3X1xkG8DChTNm0z7KryGwjVxBW$
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconducto
>> r
>> .org_packages_release_bioc_html_COHCAP.html=DwMGaQ=eRAMFD45gAfqt8
>> 4 
>> VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJ

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Hervé Pagès]

It is not clear what the purpose of these "if" statement is. Apparently 
to set the $os_name variable but then where is this variable used and 
for what?


So you might want to revisit the need for these tests. Maybe you don't 
need them after all.


Another problem is that the temporary files generated by your Perl 
scripts are generated in the current working directory. As discussed 
earlier, this is not good. Please make sure that all temporary files are 
generated in tempdir().


Thanks!
H.


On 4/28/20 10:43, Charles Warden wrote:

Hi H,

Thank you for pointing that out.

I am currently not seeing errors on my Windows computer, but I see that I need to add 
"msys" for Windows on your system (and add quotes as well as make the error 
message more clear).  I have a 64-bit Windows computer and I didn't get an error message, 
but I can see how this could cause problems.  I apologize for not realizing that.

It sounds like I should wait a little while to do that.  However, I think this 
does sound correct, and I will make that change.

Thank You,
Charles

-Original Message-
From: Hervé Pagès 
Sent: Tuesday, April 28, 2020 10:32 AM
To: Charles Warden ; Shepherd, Lori ; 
'bioc-devel@r-project.org' 
Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi Charles,

The error you get on Windows is because your Perl script integrate_island.pl 
fails on this platform. It contains the following code:

if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
  {
  #Mac
  $os_name = "MAC";
  }#end if ($os eq "MacOS")
elsif ($os eq "MSWin32")
  {
  #PC
  $os_name = "PC";
  }#end if ($os eq "MacOS")
else
  {
  print "Need to specify folder structure for $os!\n";
  exit;
  }#end else

The major problem with this code is that the script will exit
**normally** without doing anything if the detected OS is not one of the 
expected ones. So the 'temp_paired_367853.txt' file is not produced and your R 
code later fails to open it (when you try to read the file with read.table()).

Note that before exiting, your Perl script displays:

Need to specify folder structure for msys!

which you can see in the report. This gives you a BIG clue of what the problem 
is and how to fix it.

If you develop your package on Windows (and it seems you do), the problem 
should be very reproducible for you, granted that you use R
4.0.0 for that of course.

Thanks,
H.


On 4/28/20 09:02, Charles Warden wrote:

Hi Lori,

Thank you very much.

I was thinking about reverting the change to test not specifying the
full file path at one point (in *v1.33.6*), but I was planning on
keeping the change to using a temporary directory in *v1.33.4*.
Essentially, I tested making that change in *v1.33.6* because there
was still an error message in *v1.33.4.*

However, I will wait to see what else you suggest, before making any
additional changes.  From my end, there is no need to rush, and I can
wait until next week (or later).

You probably already know this, but it looks like *v1.33.6 *is in the
release version without any errors (although it does look like the
Windows version is different):

https://urldefense.com/v3/__https://www.bioconductor.org/packages/rele
ase/bioc/html/COHCAP.html__;!!Fou38LsQmgU!_wdP4PPRbzvocGetxQ4gXCipwd4_
1cOH4l3X1xkG8DChTNm0z7KryGwjVxBW$
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor
.org_packages_release_bioc_html_COHCAP.html=DwMGaQ=eRAMFD45gAfqt84
VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=OANP0q_4ipib1q
0Y0KadeY9Api_-E4mZFZDodVQ8gMY=9TOVgc79RcLRStlZDJLBYL-wmdRF4rBN6aWrEG
gHdGQ=>

So, if I understand everything, I think this is OK.

Thanks Again,

Charles

*From:*Shepherd, Lori 
*Sent:* Tuesday, April 28, 2020 5:29 AM
*To:* Charles Warden ; Hervé Pagès
; 'bioc-devel@r-project.org'

*Subject:* Re: [Bioc-devel] Windows Development Build Error Message
for COHCAP

I can investigate more on the windows machine after we are done with
the release (later this week -- possibly early next)

   I would highly recommend not reverting the change to using a
temporary directory.  We don't normally allow anyone to write to
anywhere but a temporary directory except in extreme circumstances.
New packages that are reviewed would not get accepted in Bioconductor if they 
did this.

We appreciate your effort on trying to debug this and will help you
shortly.

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

--
--

*From:*Charles Warden mailto:cwar...@coh.org>>
*Sent:* Monday, April 27, 2020 12:27 PM

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Charles Warden]

Hi H,

Thank you for pointing that out.

I am currently not seeing errors on my Windows computer, but I see that I need 
to add "msys" for Windows on your system (and add quotes as well as make the 
error message more clear).  I have a 64-bit Windows computer and I didn't get 
an error message, but I can see how this could cause problems.  I apologize for 
not realizing that.

It sounds like I should wait a little while to do that.  However, I think this 
does sound correct, and I will make that change.

Thank You,
Charles

-Original Message-
From: Hervé Pagès  
Sent: Tuesday, April 28, 2020 10:32 AM
To: Charles Warden ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi Charles,

The error you get on Windows is because your Perl script integrate_island.pl 
fails on this platform. It contains the following code:

if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
 {
 #Mac
 $os_name = "MAC";
 }#end if ($os eq "MacOS")
elsif ($os eq "MSWin32")
 {
 #PC
 $os_name = "PC";
 }#end if ($os eq "MacOS")
else
 {
 print "Need to specify folder structure for $os!\n";
 exit;
 }#end else

The major problem with this code is that the script will exit
**normally** without doing anything if the detected OS is not one of the 
expected ones. So the 'temp_paired_367853.txt' file is not produced and your R 
code later fails to open it (when you try to read the file with read.table()).

Note that before exiting, your Perl script displays:

   Need to specify folder structure for msys!

which you can see in the report. This gives you a BIG clue of what the problem 
is and how to fix it.

If you develop your package on Windows (and it seems you do), the problem 
should be very reproducible for you, granted that you use R
4.0.0 for that of course.

Thanks,
H.


On 4/28/20 09:02, Charles Warden wrote:
> Hi Lori,
> 
> Thank you very much.
> 
> I was thinking about reverting the change to test not specifying the 
> full file path at one point (in *v1.33.6*), but I was planning on 
> keeping the change to using a temporary directory in *v1.33.4*.
> Essentially, I tested making that change in *v1.33.6* because there 
> was still an error message in *v1.33.4.*
> 
> However, I will wait to see what else you suggest, before making any 
> additional changes.  From my end, there is no need to rush, and I can 
> wait until next week (or later).
> 
> You probably already know this, but it looks like *v1.33.6 *is in the 
> release version without any errors (although it does look like the 
> Windows version is different):
> 
> https://urldefense.com/v3/__https://www.bioconductor.org/packages/rele
> ase/bioc/html/COHCAP.html__;!!Fou38LsQmgU!_wdP4PPRbzvocGetxQ4gXCipwd4_
> 1cOH4l3X1xkG8DChTNm0z7KryGwjVxBW$ 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor
> .org_packages_release_bioc_html_COHCAP.html=DwMGaQ=eRAMFD45gAfqt84
> VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=OANP0q_4ipib1q
> 0Y0KadeY9Api_-E4mZFZDodVQ8gMY=9TOVgc79RcLRStlZDJLBYL-wmdRF4rBN6aWrEG
> gHdGQ=>
> 
> So, if I understand everything, I think this is OK.
> 
> Thanks Again,
> 
> Charles
> 
> *From:*Shepherd, Lori 
> *Sent:* Tuesday, April 28, 2020 5:29 AM
> *To:* Charles Warden ; Hervé Pagès 
> ; 'bioc-devel@r-project.org'
> 
> *Subject:* Re: [Bioc-devel] Windows Development Build Error Message 
> for COHCAP
> 
> I can investigate more on the windows machine after we are done with 
> the release (later this week -- possibly early next)
> 
>   I would highly recommend not reverting the change to using a 
> temporary directory.  We don't normally allow anyone to write to 
> anywhere but a temporary directory except in extreme circumstances.  
> New packages that are reviewed would not get accepted in Bioconductor if they 
> did this.
> 
> We appreciate your effort on trying to debug this and will help you 
> shortly.
> 
> Cheers,
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> ----------
> --
> 
> *From:*Charles Warden mailto:cwar...@coh.org>>
> *Sent:* Monday, April 27, 2020 12:27 PM
> *To:* Hervé Pagès  <mailto:hpa...@fredhutch.org>>; Shepherd, Lori 
> mailto:lori.sheph...@roswellpark.org>>; 
> 'bioc-devel@r-project.org'
> mailto:bioc-devel@r-project

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Hervé Pagès]

Hi Charles,

The error you get on Windows is because your Perl script 
integrate_island.pl fails on this platform. It contains the following code:


if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
{
#Mac
$os_name = "MAC";
}#end if ($os eq "MacOS")
elsif ($os eq "MSWin32")
{
#PC
$os_name = "PC";
}#end if ($os eq "MacOS")
else
{
print "Need to specify folder structure for $os!\n";
exit;
}#end else

The major problem with this code is that the script will exit 
**normally** without doing anything if the detected OS is not one of the 
expected ones. So the 'temp_paired_367853.txt' file is not produced and 
your R code later fails to open it (when you try to read the file with 
read.table()).


Note that before exiting, your Perl script displays:

  Need to specify folder structure for msys!

which you can see in the report. This gives you a BIG clue of what the 
problem is and how to fix it.


If you develop your package on Windows (and it seems you do), the 
problem should be very reproducible for you, granted that you use R 
4.0.0 for that of course.


Thanks,
H.


On 4/28/20 09:02, Charles Warden wrote:

Hi Lori,

Thank you very much.

I was thinking about reverting the change to test not specifying the 
full file path at one point (in *v1.33.6*), but I was planning on 
keeping the change to using a temporary directory in *v1.33.4*.  
Essentially, I tested making that change in *v1.33.6* because there was 
still an error message in *v1.33.4.*


However, I will wait to see what else you suggest, before making any 
additional changes.  From my end, there is no need to rush, and I can 
wait until next week (or later).


You probably already know this, but it looks like *v1.33.6 *is in the 
release version without any errors (although it does look like the 
Windows version is different):


https://www.bioconductor.org/packages/release/bioc/html/COHCAP.html 
<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_packages_release_bioc_html_COHCAP.html=DwMGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=OANP0q_4ipib1q0Y0KadeY9Api_-E4mZFZDodVQ8gMY=9TOVgc79RcLRStlZDJLBYL-wmdRF4rBN6aWrEGgHdGQ=>


So, if I understand everything, I think this is OK.

Thanks Again,

Charles

*From:*Shepherd, Lori 
*Sent:* Tuesday, April 28, 2020 5:29 AM
*To:* Charles Warden ; Hervé Pagès 
; 'bioc-devel@r-project.org' 

*Subject:* Re: [Bioc-devel] Windows Development Build Error Message for 
COHCAP


I can investigate more on the windows machine after we are done with the 
release (later this week -- possibly early next)


  I would highly recommend not reverting the change to using a temporary 
directory.  We don't normally allow anyone to write to anywhere but a 
temporary directory except in extreme circumstances.  New packages that 
are reviewed would not get accepted in Bioconductor if they did this.


We appreciate your effort on trying to debug this and will help you 
shortly.


Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263



*From:*Charles Warden mailto:cwar...@coh.org>>
*Sent:* Monday, April 27, 2020 12:27 PM
*To:* Hervé Pagès mailto:hpa...@fredhutch.org>>; 
Shepherd, Lori <mailto:lori.sheph...@roswellpark.org>>; 'bioc-devel@r-project.org' 
mailto:bioc-devel@r-project.org>>
*Subject:* RE: [Bioc-devel] Windows Development Build Error Message for 
COHCAP


Hi,

I am not sure if I am going to have to wait to submit extra revisions.  
However, I am unfortunately having the same issue (even though I tested 
using the temporary directory instead of the current working directory, 
in COHCAP (v.1.33.4).


I also tested changing the file path to the temporary in v.1.33.6, but 
that also didn't fix the problem (and I might change that back).


I am also still not able to reproduce this error message on my end.

For example, this is what the output of the build command looks like:

C:\Users\Charles\Documents>"C:\Program Files\R\R-4.0.0\bin\R.exe" CMD 
build COHCAP

* checking for file 'COHCAP/DESCRIPTION' ... OK
* preparing 'COHCAP':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'COHCAP_1.33.6.tar.gz'

And, I can also install COHCAP successfully using devtools (in R-4.0.0), 
although it does have some warnings:



library("devtools")

Loading required package

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Charles Warden]

Hi Lori,

Thank you very much.

I was thinking about reverting the change to test not specifying the full file 
path at one point (in v1.33.6), but I was planning on keeping the change to 
using a temporary directory in v1.33.4.  Essentially, I tested making that 
change in v1.33.6 because there was still an error message in  v1.33.4.

However, I will wait to see what else you suggest, before making any additional 
changes.  From my end, there is no need to rush, and I can wait until next week 
(or later).

You probably already know this, but it looks like v1.33.6 is in the release 
version without any errors (although it does look like the Windows version is 
different):

https://www.bioconductor.org/packages/release/bioc/html/COHCAP.html

So, if I understand everything, I think this is OK.

Thanks Again,
Charles

From: Shepherd, Lori 
Sent: Tuesday, April 28, 2020 5:29 AM
To: Charles Warden ; Hervé Pagès ; 
'bioc-devel@r-project.org' 
Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

I can investigate more on the windows machine after we are done with the 
release (later this week -- possibly early next)

 I would highly recommend not reverting the change to using a temporary 
directory.  We don't normally allow anyone to write to anywhere but a temporary 
directory except in extreme circumstances.  New packages that are reviewed 
would not get accepted in Bioconductor if they did this.


We appreciate your effort on trying to debug this and will help you shortly.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Charles Warden mailto:cwar...@coh.org>>
Sent: Monday, April 27, 2020 12:27 PM
To: Hervé Pagès mailto:hpa...@fredhutch.org>>; Shepherd, 
Lori mailto:lori.sheph...@roswellpark.org>>; 
'bioc-devel@r-project.org' 
mailto:bioc-devel@r-project.org>>
Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I am not sure if I am going to have to wait to submit extra revisions.  
However, I am unfortunately having the same issue (even though I tested using 
the temporary directory instead of the current working directory, in COHCAP 
(v.1.33.4).

I also tested changing the file path to the temporary in v.1.33.6, but that 
also didn't fix the problem (and I might change that back).

I am also still not able to reproduce this error message on my end.

For example, this is what the output of the build command looks like:

C:\Users\Charles\Documents>"C:\Program Files\R\R-4.0.0\bin\R.exe" CMD build 
COHCAP
* checking for file 'COHCAP/DESCRIPTION' ... OK
* preparing 'COHCAP':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'COHCAP_1.33.6.tar.gz'

And, I can also install COHCAP successfully using devtools (in R-4.0.0), 
although it does have some warnings:

> library("devtools")
Loading required package: usethis
> devtools::install_github("cwarden45/COHCAP")
Skipping install of 'COHCAP' from a github remote, the SHA1 (09b017ba) has not 
changed since last install.
  Use `force = TRUE` to force installation
> devtools::install_github("cwarden45/COHCAP", force=TRUE)
Downloading GitHub repo cwarden45/COHCAP@master



   checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 ...

   checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 ...

√  checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 (339ms)




-  preparing 'COHCAP':
   checking DESCRIPTION meta-information ...

   checking DESCRIPTION meta-information ...

√  checking DESCRIPTION meta-information
-  cleaning src




-  checking for LF line-endings in source and make files and shell scripts




-  checking for empty or unneeded directories




-  building 'COHCAP_1.33.6.tar.gz'




Installing package into ‘C:/Users/Charles/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'COHCAP' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.0/include" 
-DNDEBUG  -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include' 
-I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include'-O2 -Wall  
-mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.0/include" 
-DNDEBUG  -I'C:/Users/Charles/Docume

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

I can investigate more on the windows machine after we are done with the 
release (later this week -- possibly early next)

 I would highly recommend not reverting the change to using a temporary 
directory.  We don't normally allow anyone to write to anywhere but a temporary 
directory except in extreme circumstances.  New packages that are reviewed 
would not get accepted in Bioconductor if they did this.


We appreciate your effort on trying to debug this and will help you shortly.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Charles Warden 
Sent: Monday, April 27, 2020 12:27 PM
To: Herv�� Pag��s ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I am not sure if I am going to have to wait to submit extra revisions.  
However, I am unfortunately having the same issue (even though I tested using 
the temporary directory instead of the current working directory, in COHCAP 
(v.1.33.4).

I also tested changing the file path to the temporary in v.1.33.6, but that 
also didn't fix the problem (and I might change that back).

I am also still not able to reproduce this error message on my end.

For example, this is what the output of the build command looks like:

C:\Users\Charles\Documents>"C:\Program Files\R\R-4.0.0\bin\R.exe" CMD build 
COHCAP
* checking for file 'COHCAP/DESCRIPTION' ... OK
* preparing 'COHCAP':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'COHCAP_1.33.6.tar.gz'

And, I can also install COHCAP successfully using devtools (in R-4.0.0), 
although it does have some warnings:

> library("devtools")
Loading required package: usethis
> devtools::install_github("cwarden45/COHCAP")
Skipping install of 'COHCAP' from a github remote, the SHA1 (09b017ba) has not 
changed since last install.
  Use `force = TRUE` to force installation
> devtools::install_github("cwarden45/COHCAP", force=TRUE)
Downloading GitHub repo cwarden45/COHCAP@master



   checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 ...

   checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 ...

��  checking for file 
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
 (339ms)




-  preparing 'COHCAP':
   checking DESCRIPTION meta-information ...

   checking DESCRIPTION meta-information ...

��  checking DESCRIPTION meta-information
-  cleaning src




-  checking for LF line-endings in source and make files and shell scripts




-  checking for empty or unneeded directories




-  building 'COHCAP_1.33.6.tar.gz'




Installing package into ��C:/Users/Charles/Documents/R/win-library/4.0��
(as ��lib�� is unspecified)
* installing *source* package 'COHCAP' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.0/include" 
-DNDEBUG  -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include' 
-I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include'-O2 -Wall  
-mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-40~1.0/include" 
-DNDEBUG  -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include' 
-I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include'-O2 -Wall  
-mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ANOVA.cpp -o Rcpp_BH_ANOVA.o
In file included from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_/na_assert.hpp:23,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/arg.hpp:25,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/placeholders.hpp:24,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/apply.hpp:24,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find_if.hpp:17,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find.hpp:17,
 from 
C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_/contains_impl.hpp:20,

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Charles Warden]

cessary parentheses in declaration of 'assert_not_arg' 
[-Wparentheses]
 failed  (boost::mpl::not_::
 ^
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o 
COHCAP.dll tmp.def RcppExports.o Rcpp_BH_ANOVA.o Rcpp_BH_linear_regression.o 
Rcpp_BH_ttest.o -LC:/PROGRA~1/R/R-40~1.0/bin/x64 -lR
installing to 
C:/Users/Charles/Documents/R/win-library/4.0/00LOCK-COHCAP/00new/COHCAP/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'COHCAP'
finding HTML links ... done
COHCAP.BSSeq.preprocess html  
COHCAP.BSSeq_V2.methyl.tablehtml  
COHCAP.annotate html  
COHCAP.avg.by.islandhtml  
COHCAP.avg.by.site  html  
COHCAP.denovo   html  
COHCAP.integrate.avg.by.island  html  
COHCAP.integrate.avg.by.sitehtml  
COHCAP.qc   html  
COHCAP.reformatFinalReport  html  
COHCAP.site html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COHCAP)

The downloaded source packages are in
‘C:\Users\Charles\AppData\Local\Temp\Rtmp88lsk0\downloaded_packages’
Installation path not writeable, unable to update packages: boot, class,
  foreign, KernSmooth, MASS, nnet, spatial

I am not sure if this last warning about the installation path has something to 
do with using both the pre-release (previously) and release (currently) 
versions of R-4.0.0.

Can you please help me know if you have any other troubleshooting suggestions 
for the Window server used to test the Bioconductor packages?

Thank You,
Charles

-Original Message-
From: Hervé Pagès  
Sent: Thursday, April 23, 2020 12:23 PM
To: Charles Warden ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Attention: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.]

--
Hi Charles,

On 4/23/20 10:19, Charles Warden wrote:

> My guess was that creating the temporary file in the working directory 
> instead of another folder might help.

FWIW here are 2 important reasons for writing temporary stuff to
tempdir() instead of the current working directory:

1. tempdir() is the only place that is guaranteed to be writable on every 
system. Yes the user home is very likely to be writable too but there is 
actually no guarantee and some systems have unconventional setups where it's 
not.

2. Whatever you put in tempdir() will automatically be removed at the end of 
the R session. Even though there are ways to achieve this with the temporary 
stuff you write in the user home, it's not automatic and hard to get right.

Cheers,
H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

--

-SECURITY/CONFIDENTIALITY WARNING-  

This message and any attachments are intended solely for the individual or 
entity to which they are addressed. This communication may contain information 
that is privileged, confidential, or exempt from disclosure under applicable 
law (e.g., personal health information, research data, financial information). 
Because this e-mail has been sent without encryption, individuals other than 
the intended recipient may be able to view the information, forward it to 
others or tamper with the information without the knowledge or consent of the 
sender. If you are not the intended recipient, or the employee or person 
responsible for delivering the message to the intended recipient, any 
dissemination, distribution or copying of the communication is strictly 
prohibited. If you received the communication in error, please notify the 
sender immediately by replying to this message and deleting the message and any 
accompanying files from your system. If, due to the security risks, you do not 
wish to receive further communications via e-mail, please reply to this message 
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Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Charles Warden]

Hi H,

Thank you for the additional information.

I have pushed the git updates using tempdir() instead of getwd().  It sounds 
like that will probably fix the problem, and I will check tomorrow.

Best Wishes,
Charles

-Original Message-
From: Hervé Pagès  
Sent: Thursday, April 23, 2020 12:23 PM
To: Charles Warden ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Attention: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.]

--
Hi Charles,

On 4/23/20 10:19, Charles Warden wrote:

> My guess was that creating the temporary file in the working directory 
> instead of another folder might help.

FWIW here are 2 important reasons for writing temporary stuff to
tempdir() instead of the current working directory:

1. tempdir() is the only place that is guaranteed to be writable on every 
system. Yes the user home is very likely to be writable too but there is 
actually no guarantee and some systems have unconventional setups where it's 
not.

2. Whatever you put in tempdir() will automatically be removed at the end of 
the R session. Even though there are ways to achieve this with the temporary 
stuff you write in the user home, it's not automatic and hard to get right.

Cheers,
H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

--

-SECURITY/CONFIDENTIALITY WARNING-  

This message and any attachments are intended solely for the individual or 
entity to which they are addressed. This communication may contain information 
that is privileged, confidential, or exempt from disclosure under applicable 
law (e.g., personal health information, research data, financial information). 
Because this e-mail has been sent without encryption, individuals other than 
the intended recipient may be able to view the information, forward it to 
others or tamper with the information without the knowledge or consent of the 
sender. If you are not the intended recipient, or the employee or person 
responsible for delivering the message to the intended recipient, any 
dissemination, distribution or copying of the communication is strictly 
prohibited. If you received the communication in error, please notify the 
sender immediately by replying to this message and deleting the message and any 
accompanying files from your system. If, due to the security risks, you do not 
wish to receive further communications via e-mail, please reply to this message 
and inform the sender that you do not wish to receive further e-mail from the 
sender. (LCP301)

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Hervé Pagès]

Hi Charles,

On 4/23/20 10:19, Charles Warden wrote:


My guess was that creating the temporary file in the working directory instead 
of another folder might help.


FWIW here are 2 important reasons for writing temporary stuff to 
tempdir() instead of the current working directory:


1. tempdir() is the only place that is guaranteed to be writable on 
every system. Yes the user home is very likely to be writable too but 
there is actually no guarantee and some systems have unconventional 
setups where it's not.


2. Whatever you put in tempdir() will automatically be removed at the 
end of the R session. Even though there are ways to achieve this with 
the temporary stuff you write in the user home, it's not automatic and 
hard to get right.


Cheers,
H.

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

In your vignette you also use   `getwd()`  to define your output directory.  
Please change this to use a temporary directory  `tempdir()`


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Thursday, April 23, 2020 8:00 AM
To: Charles Warden ; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Thank you for your inquiry

R 4.0.0 can be downloaed from the following page. This patched page exists a 
few weeks out from the official R release for the patched version of R windows:


https://secure-web.cisco.com/1rVmbsYV5l6Byh8Yxia7uE_vjkELNEv9x-phlPOD4JZps4zzXWvkm5y5iT6tN_xdLE5OKhw5aFcayOxFdH1TZaOdeZSnP4jNV20TSyigyof9gxL32zvj2VKmeAycLaq__vn63nmNQcrcNfrV307jWUNM0QeREQq8TO7cM1fYdIpG1-OKb47JpH7YMFZqJyWENSteiqzz76lEINnJxX5SIY6_YknZtLWp8xRWkVjlTNKiT72Y6eAPRrCvC9FN1_Gqz4logMBLltKQBvUBbE7JY99_EtVCHLQqhmnbGg4dVxKOD75bWlau_K7grnxO6NCbAOjFnVUHVM-IEkSQruW_KPA/https%3A%2F%2Fcran.r-project.org%2Fbin%2Fwindows%2Fbase%2Frpatched.html


2.  Landing pages can have different versions of the file for different 
platforms when a package will build cleanly for one platform but not another.  
We only propagate and make available successfully built packages.


3.  You can wait a day or two if you like but realize the 3.11 release is fast 
approaching.  If this stay ERROR and it is not fixed by monday you will have to 
push fixes to both a release 3.11 and the new devel branch (master branch 
prepping for 3.12 in fall).


4.  I'll try and log on our windows builder later today to see if I can track 
down any additional information for you to help debug.  If I find anything I 
will contact you about it.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Charles Warden 

Sent: Wednesday, April 22, 2020 12:00 PM
To: 'bioc-devel@r-project.org' 
Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://secure-web.cisco.com/14soK-lir-qt5k3KJCJKxxSPwdESxh91c_rkfAkfpDOqOUvXzM0n9MzRO_j5W5YsMzlMpHKj8hD4qgXS8qgJycZANUXuMoVlTuxKCDTotDQku3EGNvVwLIWjyC4ZeIDnSRnFJE4KnTbacOABfRotIDmjhuZqWJmXADjmoBsUTEpAhwIEMAHLe-De7YiQGt-OJNvo_Op4ArktJnzOfxhWMOUG0kZvelbmwKwV_MmvFVJpgOljB5EAcUHLuOLpvN1dlH5gsWhslkm1FvMX9gmvNJ2y0T3onSd5pHZ2FbwM8-8sgSPEbuxXjtT1WQUYyFdqUIBNQY7Xv8iEdEBt1q7qVTw/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FCOHCAP%2Ftokay2-buildsrc.html

I changed the default settings to avoid an earlier error message (again, just 
on Windows), but I am currently getting an error message that I am having some 
trouble reproducing.

Can you help me with either of the following questions?


  1.  I apologize for the simple question, but where can I download the Windows 
executable for R-4.0.0?  I was able to reproduce and fix an earlier issue with 
R-devel (on Linux), but I was not certain how to get the error message for 
Windows.  I have tried to reproduce the error using the devtools installation 
from the GitHub code 
(https://secure-web.cisco.com/1CMIdB2_FCZaFouyijL6DJBleIv1z6kjb0vJp48UqtfezzRyresTr07xJ9yP83U_HqxDPiTYbIIG_3bYDlfcvr9QH832g8VnWkkNG5dK1P2qxQbm9OWI_b3EERjUTwhY2H8cb6Lsko1ITsutzNvWoL_Dp_fvzUxN0nDwb6eghpCrMMy6ndFekSqrQdkZO0IhVKxvMXODM3MkIZRsiEaomyhKOn6lUKila6pgUgDSfQ9PypaW7BcQcWhGb9U-f8TL9fvtbUqBaB83MoDiXfJKsO_UoJLrlyh8sR6wJ5tNHkt3e-7uUwzz6H360PSI3rxp1a5gXTxLcMp9ymSQR6UF1CQ/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP),
 but that can be installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different 
(http://secure-web.cisco.com/1L5TyDrJci1NAZMGxCrXIKm2wn3kgWC_9LSEIs73dOegI5BFj7AhvLaYz0i17qdT2pElt5CByZhFvxEMQ2Uunp62vwJ4s_-0G-gi1gOdMQ9Z_rf-1WN7sEym8bdEQgX4sO0SE8JaTNDZUG-zwsHvCZJP6ZYlq4valW3HrFbWU8PbZ5_9r-zCQUNwVxenocEirsb8kzp5kABBj0hI9c9EvH1C2o0oAQ0O9sIKULrkHAmQqjUg3cS8axxnfC_GUNGY2Be1EHLD0Na98zDHgOce95-bK82bGVtTnR5g2ynyW9qcQqeG0SD0_LuQo3YEkSPh3gptJfBs-_myNtkqDePCZCg/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FCOHCAP.html),
 where I see cohcap_1.33.1.zip for Windows.  I think I saw the first error 
message in 1.33.1, and I made an intermediate change before changing the 
defaults to avoid the error message.  However, the strange thing was that I 
thought I saw an "OK" status while I was waiting for the 1.33.3 version to 
appear in the build reports (which I thought was for COHCAP 1.33.2).  Do all of 
the packages get re-built, regardless of whether an update is uploaded?
 *   I am wondering if there is a chance that I might be able to wait a day 
o

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

Thank you for your inquiry

R 4.0.0 can be downloaed from the following page. This patched page exists a 
few weeks out from the official R release for the patched version of R windows:


https://cran.r-project.org/bin/windows/base/rpatched.html


2.  Landing pages can have different versions of the file for different 
platforms when a package will build cleanly for one platform but not another.  
We only propagate and make available successfully built packages.


3.  You can wait a day or two if you like but realize the 3.11 release is fast 
approaching.  If this stay ERROR and it is not fixed by monday you will have to 
push fixes to both a release 3.11 and the new devel branch (master branch 
prepping for 3.12 in fall).


4.  I'll try and log on our windows builder later today to see if I can track 
down any additional information for you to help debug.  If I find anything I 
will contact you about it.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Charles Warden 

Sent: Wednesday, April 22, 2020 12:00 PM
To: 'bioc-devel@r-project.org' 
Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://secure-web.cisco.com/14soK-lir-qt5k3KJCJKxxSPwdESxh91c_rkfAkfpDOqOUvXzM0n9MzRO_j5W5YsMzlMpHKj8hD4qgXS8qgJycZANUXuMoVlTuxKCDTotDQku3EGNvVwLIWjyC4ZeIDnSRnFJE4KnTbacOABfRotIDmjhuZqWJmXADjmoBsUTEpAhwIEMAHLe-De7YiQGt-OJNvo_Op4ArktJnzOfxhWMOUG0kZvelbmwKwV_MmvFVJpgOljB5EAcUHLuOLpvN1dlH5gsWhslkm1FvMX9gmvNJ2y0T3onSd5pHZ2FbwM8-8sgSPEbuxXjtT1WQUYyFdqUIBNQY7Xv8iEdEBt1q7qVTw/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FCOHCAP%2Ftokay2-buildsrc.html

I changed the default settings to avoid an earlier error message (again, just 
on Windows), but I am currently getting an error message that I am having some 
trouble reproducing.

Can you help me with either of the following questions?


  1.  I apologize for the simple question, but where can I download the Windows 
executable for R-4.0.0?  I was able to reproduce and fix an earlier issue with 
R-devel (on Linux), but I was not certain how to get the error message for 
Windows.  I have tried to reproduce the error using the devtools installation 
from the GitHub code 
(https://secure-web.cisco.com/1CMIdB2_FCZaFouyijL6DJBleIv1z6kjb0vJp48UqtfezzRyresTr07xJ9yP83U_HqxDPiTYbIIG_3bYDlfcvr9QH832g8VnWkkNG5dK1P2qxQbm9OWI_b3EERjUTwhY2H8cb6Lsko1ITsutzNvWoL_Dp_fvzUxN0nDwb6eghpCrMMy6ndFekSqrQdkZO0IhVKxvMXODM3MkIZRsiEaomyhKOn6lUKila6pgUgDSfQ9PypaW7BcQcWhGb9U-f8TL9fvtbUqBaB83MoDiXfJKsO_UoJLrlyh8sR6wJ5tNHkt3e-7uUwzz6H360PSI3rxp1a5gXTxLcMp9ymSQR6UF1CQ/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP),
 but that can be installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different 
(http://secure-web.cisco.com/1L5TyDrJci1NAZMGxCrXIKm2wn3kgWC_9LSEIs73dOegI5BFj7AhvLaYz0i17qdT2pElt5CByZhFvxEMQ2Uunp62vwJ4s_-0G-gi1gOdMQ9Z_rf-1WN7sEym8bdEQgX4sO0SE8JaTNDZUG-zwsHvCZJP6ZYlq4valW3HrFbWU8PbZ5_9r-zCQUNwVxenocEirsb8kzp5kABBj0hI9c9EvH1C2o0oAQ0O9sIKULrkHAmQqjUg3cS8axxnfC_GUNGY2Be1EHLD0Na98zDHgOce95-bK82bGVtTnR5g2ynyW9qcQqeG0SD0_LuQo3YEkSPh3gptJfBs-_myNtkqDePCZCg/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FCOHCAP.html),
 where I see cohcap_1.33.1.zip for Windows.  I think I saw the first error 
message in 1.33.1, and I made an intermediate change before changing the 
defaults to avoid the error message.  However, the strange thing was that I 
thought I saw an "OK" status while I was waiting for the 1.33.3 version to 
appear in the build reports (which I thought was for COHCAP 1.33.2).  Do all of 
the packages get re-built, regardless of whether an update is uploaded?
 *   I am wondering if there is a chance that I might be able to wait a day 
or two and see if I can get a status of "OK" for all steps on all of the test 
servers.  However, if that is true, then I am a little worried about what 
happens if there is a temporary error in the release version.


Thank you very much!

Sincerely,
Charles
Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375

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law (e.g., personal health information, research data, fina

[Bioc-devel] Windows Development Build Error Message for COHCAP

[Charles Warden]

Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://bioconductor.org/checkResults/devel/bioc-LATEST/COHCAP/tokay2-buildsrc.html

I changed the default settings to avoid an earlier error message (again, just 
on Windows), but I am currently getting an error message that I am having some 
trouble reproducing.

Can you help me with either of the following questions?


  1.  I apologize for the simple question, but where can I download the Windows 
executable for R-4.0.0?  I was able to reproduce and fix an earlier issue with 
R-devel (on Linux), but I was not certain how to get the error message for 
Windows.  I have tried to reproduce the error using the devtools installation 
from the GitHub code (https://github.com/cwarden45/COHCAP), but that can be 
installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different 
(http://bioconductor.org/packages/3.11/bioc/html/COHCAP.html), where I see 
cohcap_1.33.1.zip for Windows.  I think I saw the first error message in 
1.33.1, and I made an intermediate change before changing the defaults to avoid 
the error message.  However, the strange thing was that I thought I saw an "OK" 
status while I was waiting for the 1.33.3 version to appear in the build 
reports (which I thought was for COHCAP 1.33.2).  Do all of the packages get 
re-built, regardless of whether an update is uploaded?
 *   I am wondering if there is a chance that I might be able to wait a day 
or two and see if I can get a status of "OK" for all steps on all of the test 
servers.  However, if that is true, then I am a little worried about what 
happens if there is a temporary error in the release version.


Thank you very much!

Sincerely,
Charles
Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375

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Re: [Bioc-devel] Windows only vignette error - any ideas?

[Andrzej Oleś]

To me this issue doesn't seem to be directly linked to BiocStyle as the
affected package does not depend on it. Might be still a problem with
rmarkdown though.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 10:12 PM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> We are hoping it is related to this:
> https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html so
> you should just sit tight.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  on behalf of
> Christopher John 
> Sent: Wednesday, December 4, 2019 2:05 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Windows only vignette error - any ideas?
>
> Hi
>
> Since this morning I am getting an error for the Windows build only of my
> M3C package, shown below.
>
> Could anyone help please?
>
> Thanks,
>
> Chris
>
> * checking for file 'M3C/DESCRIPTION' ... OK
> * preparing 'M3C':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building 'M3Cvignette.Rmd' using rmarkdown
> ! Package ifvtex Error: Name clash, \ifvtex is already defined.
>
> Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics:
> Failed to compile M3Cvignette.tex. See
> https://yihui.name/tinytex/r/#debugging for debugging tips. See
> M3Cvignette.log for more info.
> --- failed re-building 'M3Cvignette.Rmd'
>
> SUMMARY: processing the following file failed:
>   'M3Cvignette.Rmd'
>
> Error: Vignette re-building failed.
> Execution halted
>
> [[alternative HTML version deleted]]
>
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>
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> This email message may contain legally privileged and/or confidential
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> agent responsible for the delivery of this message to the intended
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Re: [Bioc-devel] Windows only vignette error - any ideas?

[Shepherd, Lori]

We are hoping it is related to this:  
https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html so you 
should just sit tight.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Christopher 
John 
Sent: Wednesday, December 4, 2019 2:05 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Windows only vignette error - any ideas?

Hi

Since this morning I am getting an error for the Windows build only of my
M3C package, shown below.

Could anyone help please?

Thanks,

Chris

* checking for file 'M3C/DESCRIPTION' ... OK
* preparing 'M3C':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'M3Cvignette.Rmd' using rmarkdown
! Package ifvtex Error: Name clash, \ifvtex is already defined.

Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics:
Failed to compile M3Cvignette.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips. See
M3Cvignette.log for more info.
--- failed re-building 'M3Cvignette.Rmd'

SUMMARY: processing the following file failed:
  'M3Cvignette.Rmd'

Error: Vignette re-building failed.
Execution halted

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[Bioc-devel] Windows only vignette error - any ideas?

[Christopher John]

Hi

Since this morning I am getting an error for the Windows build only of my
M3C package, shown below.

Could anyone help please?

Thanks,

Chris

* checking for file 'M3C/DESCRIPTION' ... OK
* preparing 'M3C':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'M3Cvignette.Rmd' using rmarkdown
! Package ifvtex Error: Name clash, \ifvtex is already defined.

Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics:
Failed to compile M3Cvignette.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips. See
M3Cvignette.log for more info.
--- failed re-building 'M3Cvignette.Rmd'

SUMMARY: processing the following file failed:
  'M3Cvignette.Rmd'

Error: Vignette re-building failed.
Execution halted

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[Bioc-devel] Windows vignette build error "execution failed with error code 4"

[Taner Arslan]

Dear all,

My package is almost ready to be accepted but now i am getting weird building 
error on Windows. It works without error on Linux and OS X. I have tried many 
many things. But I could not figured out.

The  error is:

Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "SubCellBarCode_files/figure-html/coverageMarkers-1.png" -trim 
"SubCellBarCode_files/figure-html/coverageMarkers-1.png"' execution failed with 
error code 4

You can see more here:
http://bioconductor.org/spb_reports/SubCellBarCode_buildreport_20190423143932.html

 I used to get this error before as well. After getting this error, when i 
resubmitted the package, the problem solved (I literally was not doing 
anything). Today i tried many times, still i get the problems. Did you ever 
encounter with this problem?

I have mac;
R version 3.5.2 (2018-12-20) ## Platform: x86_64-apple-darwin15.6.0 (64-bit) ## 
Running under: macOS Sierra 10.12.6

Thanks in advance.



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Re: [Bioc-devel] Windows-specific build error of 'seqCAT' package

[Pages, Herve]

Hi Erik,

The 'invalid class "VCFHeader" object' error on Windows has been fixed 
in Rhtslib 1.15.6.

Cheers,

H.


On 3/18/19 00:36, Erik Fasterius wrote:
> Hi, Valerie!
>
> Thanks for looking into the problem! I hope it’ll work out.
>
> Erik
>
> On 16 Mar 2019, at 22:51, Valerie Obenchain 
> mailto:obenchain.vale...@gene.com>> wrote:
>
> It doesn't look like it was the patch - the error is still there. I'll look 
> in to this some more.
> Valerie
>
> On Fri, Mar 15, 2019 at 11:10 AM Valerie Obenchain 
> mailto:obenc...@gene.com>> wrote:
> Hi Erik,
> I think the problem was introduced in a contributed patch applied to 
> VariantAnnotation in devel. I've reverted the patch and expect 
> VariantAnnotation (and downstream packages) to clear up on Windows with 
> tomorrow's builds.
> Valerie
>
> On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius 
> mailto:erik.faster...@outlook.com>> wrote:
> Hi,
>
> My seqCAT package recently broke building on the Windows platform, which I 
> assume has to do with changes to the VariantAnnotation package (upon which 
> seqCAT depends). The error (which comes during the creation of the vignette) 
> looks like this:
>
> Quitting from lines 102-112 (seqCAT.Rmd)
> Error: processing vignette 'seqCAT.Rmd' failed with diagnostics:
> invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column 
> DataFrame with names Number, Type, Description
> invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column 
> DataFrame with names Number, Type, Description
> --- failed re-building 'seqCAT.Rmd'
>
> It builds and completes all checks successfully on all other platforms, 
> though. I have no experience with Windows, so I don’t really know how to even 
> start debugging this issue (I’m working on OS X). Given that other platforms 
> are working fine I’m thinking (hoping) that this is some incompatibility with 
> recent changes to VariantAnnotation (or its dependencies) and the Windows 
> platform, but I have no clue if this is the case.
>
> Does anybody have any idea as to what is the issue here, or have any tips 
> regarding to be debug something on a different platform than the one you are 
> using yourself?
>
> Erik
>
>  [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Windows-specific build error of 'seqCAT' package

[Erik Fasterius]

Hi, Valerie!

Thanks for looking into the problem! I hope it’ll work out.

Erik

On 16 Mar 2019, at 22:51, Valerie Obenchain 
mailto:obenchain.vale...@gene.com>> wrote:

It doesn't look like it was the patch - the error is still there. I'll look in 
to this some more.
Valerie

On Fri, Mar 15, 2019 at 11:10 AM Valerie Obenchain 
mailto:obenc...@gene.com>> wrote:
Hi Erik,
I think the problem was introduced in a contributed patch applied to 
VariantAnnotation in devel. I've reverted the patch and expect 
VariantAnnotation (and downstream packages) to clear up on Windows with 
tomorrow's builds.
Valerie

On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius 
mailto:erik.faster...@outlook.com>> wrote:
Hi,

My seqCAT package recently broke building on the Windows platform, which I 
assume has to do with changes to the VariantAnnotation package (upon which 
seqCAT depends). The error (which comes during the creation of the vignette) 
looks like this:

Quitting from lines 102-112 (seqCAT.Rmd)
Error: processing vignette 'seqCAT.Rmd' failed with diagnostics:
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column 
DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column 
DataFrame with names Number, Type, Description
--- failed re-building 'seqCAT.Rmd'

It builds and completes all checks successfully on all other platforms, though. 
I have no experience with Windows, so I don’t really know how to even start 
debugging this issue (I’m working on OS X). Given that other platforms are 
working fine I’m thinking (hoping) that this is some incompatibility with 
recent changes to VariantAnnotation (or its dependencies) and the Windows 
platform, but I have no clue if this is the case.

Does anybody have any idea as to what is the issue here, or have any tips 
regarding to be debug something on a different platform than the one you are 
using yourself?

Erik

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Re: [Bioc-devel] Windows-specific build error of 'seqCAT' package

[Valerie Obenchain via Bioc-devel]

It doesn't look like it was the patch - the error is still there. I'll look
in to this some more.
Valerie

On Fri, Mar 15, 2019 at 11:10 AM Valerie Obenchain 
wrote:

> Hi Erik,
> I think the problem was introduced in a contributed patch applied to
> VariantAnnotation in devel. I've reverted the patch and expect
> VariantAnnotation (and downstream packages) to clear up on Windows with
> tomorrow's builds.
> Valerie
>
> On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius 
> wrote:
>
>> Hi,
>>
>> My seqCAT package recently broke building on the Windows platform, which
>> I assume has to do with changes to the VariantAnnotation package (upon
>> which seqCAT depends). The error (which comes during the creation of the
>> vignette) looks like this:
>>
>> Quitting from lines 102-112 (seqCAT.Rmd)
>> Error: processing vignette 'seqCAT.Rmd' failed with diagnostics:
>> invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column
>> DataFrame with names Number, Type, Description
>> invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column
>> DataFrame with names Number, Type, Description
>> --- failed re-building 'seqCAT.Rmd'
>>
>> It builds and completes all checks successfully on all other platforms,
>> though. I have no experience with Windows, so I don’t really know how to
>> even start debugging this issue (I’m working on OS X). Given that other
>> platforms are working fine I’m thinking (hoping) that this is some
>> incompatibility with recent changes to VariantAnnotation (or its
>> dependencies) and the Windows platform, but I have no clue if this is the
>> case.
>>
>> Does anybody have any idea as to what is the issue here, or have any tips
>> regarding to be debug something on a different platform than the one you
>> are using yourself?
>>
>> Erik
>>
>> [[alternative HTML version deleted]]
>>
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>>
>

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Re: [Bioc-devel] Windows-specific build error of 'seqCAT' package

[Valerie Obenchain via Bioc-devel]

Hi Erik,
I think the problem was introduced in a contributed patch applied to
VariantAnnotation in devel. I've reverted the patch and expect
VariantAnnotation (and downstream packages) to clear up on Windows with
tomorrow's builds.
Valerie

On Thu, Mar 7, 2019 at 4:10 AM Erik Fasterius 
wrote:

> Hi,
>
> My seqCAT package recently broke building on the Windows platform, which I
> assume has to do with changes to the VariantAnnotation package (upon which
> seqCAT depends). The error (which comes during the creation of the
> vignette) looks like this:
>
> Quitting from lines 102-112 (seqCAT.Rmd)
> Error: processing vignette 'seqCAT.Rmd' failed with diagnostics:
> invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column
> DataFrame with names Number, Type, Description
> invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column
> DataFrame with names Number, Type, Description
> --- failed re-building 'seqCAT.Rmd'
>
> It builds and completes all checks successfully on all other platforms,
> though. I have no experience with Windows, so I don’t really know how to
> even start debugging this issue (I’m working on OS X). Given that other
> platforms are working fine I’m thinking (hoping) that this is some
> incompatibility with recent changes to VariantAnnotation (or its
> dependencies) and the Windows platform, but I have no clue if this is the
> case.
>
> Does anybody have any idea as to what is the issue here, or have any tips
> regarding to be debug something on a different platform than the one you
> are using yourself?
>
> Erik
>
> [[alternative HTML version deleted]]
>
> ___
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[Bioc-devel] Windows-specific build error of 'seqCAT' package

[Erik Fasterius]

Hi,

My seqCAT package recently broke building on the Windows platform, which I 
assume has to do with changes to the VariantAnnotation package (upon which 
seqCAT depends). The error (which comes during the creation of the vignette) 
looks like this:

Quitting from lines 102-112 (seqCAT.Rmd)
Error: processing vignette 'seqCAT.Rmd' failed with diagnostics:
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column 
DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column 
DataFrame with names Number, Type, Description
--- failed re-building 'seqCAT.Rmd'

It builds and completes all checks successfully on all other platforms, though. 
I have no experience with Windows, so I don’t really know how to even start 
debugging this issue (I’m working on OS X). Given that other platforms are 
working fine I’m thinking (hoping) that this is some incompatibility with 
recent changes to VariantAnnotation (or its dependencies) and the Windows 
platform, but I have no clue if this is the case.

Does anybody have any idea as to what is the issue here, or have any tips 
regarding to be debug something on a different platform than the one you are 
using yourself?

Erik

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Re: [Bioc-devel] Windows error "UCSC library operation failed" in package karyoploteR

[Bernat Gel Moreno]

Ops, ok, thanks. Should have reread the documentation.

Thanks

Bernat


El 01/10/2018 a las 2:00, Dario Strbenac escribió:
> Good day,
>
> The import of BigWig files does not work on Windows and is documented. 
> Execute ?BigWigFile-class and notice in the Description section: "These 
> functions do not work on Windows.".
> --
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> ___
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Re: [Bioc-devel] Windows error "UCSC library operation failed" in package karyoploteR

[Dario Strbenac]

Good day,

The import of BigWig files does not work on Windows and is documented. Execute 
?BigWigFile-class and notice in the Description section: "These functions do 
not work on Windows.".
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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[Bioc-devel] Windows error "UCSC library operation failed" in package karyoploteR

[bernat]

Hi all,

I've got a windows only error in one example of one of my packages 
(karyoploteR).

The erroring function uses rtracklayer::import to load some data from a BigWig 
file with
  
wig.data <- rtracklayer::import(data, format = "bigWig", 
selection=plot.region[i])

where plot.region[i] is a GRanges.

The example used to use the example BigWig file from rtracklayer, but I changed 
it to
my own file to see if the problem was with the file itself. The error is 
exactly the same
with both files.

 From the error text I assume the problem might be related to reading
the data, is it correct?

Any idea of what might be failing?

This is the code of the example producing the error.


> bigwig.file <- system.file("extdata", "BRCA.genes.hg19.bw", package = 
> "karyoploteR")
> brca.genes.file <- system.file("extdata", "BRCA.genes.hg19.txt", package = 
> "karyoploteR")
> brca.genes <- toGRanges(brca.genes.file)
> seqlevelsStyle(brca.genes) <- "UCSC"
>
> kp <- plotKaryotype(zoom = brca.genes[1])
> kp <- kpPlotBigWig(kp, data=bigwig.file, r0=0, r1=0.3)
Warning in .local(object, ...) :
   Invalid argument
lseek(6, 232, invalid 'whence' value (4096)) failed
Error in .local(object, ...) : UCSC library operation failed
Calls: kpPlotBigWig ... mcols -> unlist -> summary -> summary -> .local -> .Call
Execution halted


Thanks a lot

Bernat


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Re: [Bioc-devel] Windows, normalizePath(), and non-ASCII characters

[Mike Smith]

Hi Val,

I think I achieved some resolution, if not total clarity.  It's to do with
the encoding of the of the two path variables:

> Encoding(path1)
[1] "unknown"
> Encoding(path2)
[1] "UTF-8"

I don't understand why recursive calls to normalizePath() changes the
encoding, but the combination of HDF5 & Windows fails when given UTF-8
paths.  I've updated rhdf5 to try and ensure paths are encoded in Latin-1
which Windows is fine with, but it'll still go awry if you use characters
outside that set.  I'm still searching for a more comprehensive solution.

Thanks,
Mike

On Thu, 31 May 2018 at 20:09, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Mike,
> Is this still an issue or has it been resolved?
> Val
>
>
> On 05/22/2018 02:19 PM, Mike Smith wrote:
>
> In trying to diagnose this issue athttps://support.bioconductor.org/p/108548/ 
> I've found some weird behaviour
> with Windows, normalizePath(), and non-ASCII characters.  Essentially, if I
> run normalizePath() recursively on a path that contains  'é' (I haven't
> tried other characters) something 'changes' in the string, but I can't work
> out what, and it breaks a subsequent .Call() which uses the path.
>
> The example below tries to demonstrate this in a fairly concise manner. It
> works fine if normalizePath() is run once, but fails after it's run a
> second time on itself.
>
> However, change "éxample" for "example" and both instances work. Similarly,
> both run fine on my Linux machine with the non-ASCII character inplace.
>
> I'd be grateful if anyone else with a Windows machine could verify this
> behaviour, or to shed any light on what might be the difference between path1
> and path2 below.
>
> Thank,
> Mike
>
> --
>
> ## setup some HDF5 components required later
> flags <- rhdf5:::h5checkConstants("H5F_ACC", h5default("H5F_ACC"))
> fcpl <- rhdf5:::h5checktypeAndPLC(NULL, "H5P_FILE_CREATE", allowNULL = TRUE)
> fapl <- rhdf5::H5Pcreate("H5P_FILE_ACCESS")
>
> ## create a folder with non-ASCII character
> dir.create('éxample')
> setwd("éxample")
>
> ## create two normalized paths recursively - these are 'identical'
> path1 <- normalizePath('test.h5', mustWork = FALSE)
> path2 <- normalizePath(path1, mustWork = FALSE)
> identical(path1, path2)
>
> ## create an HDF5 file using path1 - this works
> fid <- .Call("_H5Fcreate", path1, flags, fcpl@ID, fapl@ID,
>  PACKAGE = "rhdf5")
> .Call("_H5Fclose", fid, PACKAGE = "rhdf5")
> file.remove(path1)
>
> ## create an HDF5 file using path2 - this fails
> fid <- .Call("_H5Fcreate", path2, flags, fcpl@ID, fapl@ID,
>  PACKAGE = "rhdf5")
> if(exists('fid2')) {
>   .Call("_H5Fclose", fid2, PACKAGE = "rhdf5")
>   file.remove(path2)
> }
>
> ## tidy up
> rhdf5::h5closeAll()
> setwd("../")
>
>   [[alternative HTML version deleted]]
>
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>
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
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> received this message in error, please notify the sender immediately by
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Re: [Bioc-devel] Windows, normalizePath(), and non-ASCII characters

[Obenchain, Valerie]

Hi Mike,
Is this still an issue or has it been resolved?
Val


On 05/22/2018 02:19 PM, Mike Smith wrote:

In trying to diagnose this issue at
https://support.bioconductor.org/p/108548/ I've found some weird behaviour
with Windows, normalizePath(), and non-ASCII characters.  Essentially, if I
run normalizePath() recursively on a path that contains  '�' (I haven't
tried other characters) something 'changes' in the string, but I can't work
out what, and it breaks a subsequent .Call() which uses the path.

The example below tries to demonstrate this in a fairly concise manner. It
works fine if normalizePath() is run once, but fails after it's run a
second time on itself.

However, change "�xample" for "example" and both instances work. Similarly,
both run fine on my Linux machine with the non-ASCII character inplace.

I'd be grateful if anyone else with a Windows machine could verify this
behaviour, or to shed any light on what might be the difference between path1
and path2 below.

Thank,
Mike

--

## setup some HDF5 components required later
flags <- rhdf5:::h5checkConstants("H5F_ACC", h5default("H5F_ACC"))
fcpl <- rhdf5:::h5checktypeAndPLC(NULL, "H5P_FILE_CREATE", allowNULL = TRUE)
fapl <- rhdf5::H5Pcreate("H5P_FILE_ACCESS")

## create a folder with non-ASCII character
dir.create('�xample')
setwd("�xample")

## create two normalized paths recursively - these are 'identical'
path1 <- normalizePath('test.h5', mustWork = FALSE)
path2 <- normalizePath(path1, mustWork = FALSE)
identical(path1, path2)

## create an HDF5 file using path1 - this works
fid <- .Call("_H5Fcreate", path1, flags, fcpl@ID, fapl@ID,
 PACKAGE = "rhdf5")
.Call("_H5Fclose", fid, PACKAGE = "rhdf5")
file.remove(path1)

## create an HDF5 file using path2 - this fails
fid <- .Call("_H5Fcreate", path2, flags, fcpl@ID, fapl@ID,
 PACKAGE = "rhdf5")
if(exists('fid2')) {
  .Call("_H5Fclose", fid2, PACKAGE = "rhdf5")
  file.remove(path2)
}

## tidy up
rhdf5::h5closeAll()
setwd("../")

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[Bioc-devel] Windows, normalizePath(), and non-ASCII characters

[Mike Smith]

In trying to diagnose this issue at
https://support.bioconductor.org/p/108548/ I've found some weird behaviour
with Windows, normalizePath(), and non-ASCII characters.  Essentially, if I
run normalizePath() recursively on a path that contains  'é' (I haven't
tried other characters) something 'changes' in the string, but I can't work
out what, and it breaks a subsequent .Call() which uses the path.

The example below tries to demonstrate this in a fairly concise manner. It
works fine if normalizePath() is run once, but fails after it's run a
second time on itself.

However, change "éxample" for "example" and both instances work. Similarly,
both run fine on my Linux machine with the non-ASCII character inplace.

I'd be grateful if anyone else with a Windows machine could verify this
behaviour, or to shed any light on what might be the difference between path1
and path2 below.

Thank,
Mike

--

## setup some HDF5 components required later
flags <- rhdf5:::h5checkConstants("H5F_ACC", h5default("H5F_ACC"))
fcpl <- rhdf5:::h5checktypeAndPLC(NULL, "H5P_FILE_CREATE", allowNULL = TRUE)
fapl <- rhdf5::H5Pcreate("H5P_FILE_ACCESS")

## create a folder with non-ASCII character
dir.create('éxample')
setwd("éxample")

## create two normalized paths recursively - these are 'identical'
path1 <- normalizePath('test.h5', mustWork = FALSE)
path2 <- normalizePath(path1, mustWork = FALSE)
identical(path1, path2)

## create an HDF5 file using path1 - this works
fid <- .Call("_H5Fcreate", path1, flags, fcpl@ID, fapl@ID,
 PACKAGE = "rhdf5")
.Call("_H5Fclose", fid, PACKAGE = "rhdf5")
file.remove(path1)

## create an HDF5 file using path2 - this fails
fid <- .Call("_H5Fcreate", path2, flags, fcpl@ID, fapl@ID,
 PACKAGE = "rhdf5")
if(exists('fid2')) {
  .Call("_H5Fclose", fid2, PACKAGE = "rhdf5")
  file.remove(path2)
}

## tidy up
rhdf5::h5closeAll()
setwd("../")

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Re: [Bioc-devel] Windows

[Ramon Diaz-Uriarte]

And I have now asked this in R-pkg-devel
(https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html), as
suggested by Martin Maechler
(https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013169.html) in the
thread linked by Lori.

But if you can use \link{foo} (instead of \link[pkg]{foo} and
\link[pkg:bar]{foo}), as also suggested by Håkon Tjeldnes, then you should
have no problems.


Best,

R.

On Mon, 16-April-2018, at 13:16:54, Shepherd, Lori 
<lori.sheph...@roswellpark.org> wrote:
> This was also discussed in this thread a few weeks ago
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Mike Smith 
> <grimbo...@gmail.com>
> Sent: Monday, April 16, 2018 6:13:38 AM
> To: Rainer Johannes; bioc-devel
> Subject: Re: [Bioc-devel] Windows  on Tokay2>
>
> Martin mentioned that he changed the wording in
> https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
> , so more recently than your version of R-devel.
>
> Mike
>
> On 16 April 2018 at 11:57, Rainer Johannes <johannes.rai...@eurac.edu>
> wrote:
>
>> Thanks Mike,
>>
>> I somehow missed the discussion you mentioned. I would really not like to
>> include the name of the Rd file I want to link to. The *default* way that
>> works on Linux and macOS should also work on Windows - otherwise what's the
>> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
>> I don't get these warnings (R-devel from 2018-01-07 r74091).
>>
>> jo
>>
>> > On 16 Apr 2018, at 10:49, Mike Smith <grimbo...@gmail.com> wrote:
>> >
>> > Hi Johannes,
>> >
>> > xcms is certainly not alone with the warning, and it was discussed in
>> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
>> >
>> > I think you should be able to get round it by including the name of Rd
>> file you're linking to e.g.  
>> \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
>> (I haven't actually tested this though).
>> >
>> > Mike
>> >
>> > On 16 April 2018 at 09:06, Rainer Johannes <johannes.rai...@eurac.edu>
>> wrote:
>> > Dear all,
>> >
>> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
>> links in Rd files to functions and methods in other packages.
>> > Example:
>> > we have \code{\link[MSnbase]{pickPeaks}} in
>> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
>> works nicely on Linux and macOS build machines, but on tokay2 we get:
>> >
>> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
>> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
>> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
>> a topic
>> >
>> > is there any other solution to removing all links to external packages?
>> >
>> > thanks, jo
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>>
>
> [[alternative HTML version deleted]]
>
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>
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> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the employee or 
> agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
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> received this message in error, please notify the sender immediately by 
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--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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Re: [Bioc-devel] Windows

[Shepherd, Lori]

This was also discussed in this thread a few weeks ago

https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Mike Smith 
<grimbo...@gmail.com>
Sent: Monday, April 16, 2018 6:13:38 AM
To: Rainer Johannes; bioc-devel
Subject: Re: [Bioc-devel] Windows 

Martin mentioned that he changed the wording in
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.

Mike

On 16 April 2018 at 11:57, Rainer Johannes <johannes.rai...@eurac.edu>
wrote:

> Thanks Mike,
>
> I somehow missed the discussion you mentioned. I would really not like to
> include the name of the Rd file I want to link to. The *default* way that
> works on Linux and macOS should also work on Windows - otherwise what's the
> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
> I don't get these warnings (R-devel from 2018-01-07 r74091).
>
> jo
>
> > On 16 Apr 2018, at 10:49, Mike Smith <grimbo...@gmail.com> wrote:
> >
> > Hi Johannes,
> >
> > xcms is certainly not alone with the warning, and it was discussed in
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> >
> > I think you should be able to get round it by including the name of Rd
> file you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
> (I haven't actually tested this though).
> >
> > Mike
> >
> > On 16 April 2018 at 09:06, Rainer Johannes <johannes.rai...@eurac.edu>
> wrote:
> > Dear all,
> >
> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> > Example:
> > we have \code{\link[MSnbase]{pickPeaks}} in
> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
> works nicely on Linux and macOS build machines, but on tokay2 we get:
> >
> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
> >
> > is there any other solution to removing all links to external packages?
> >
> > thanks, jo
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>

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Re: [Bioc-devel] Windows

[Mike Smith]

Martin mentioned that he changed the wording in
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.

Mike

On 16 April 2018 at 11:57, Rainer Johannes 
wrote:

> Thanks Mike,
>
> I somehow missed the discussion you mentioned. I would really not like to
> include the name of the Rd file I want to link to. The *default* way that
> works on Linux and macOS should also work on Windows - otherwise what's the
> matter of the alias? Interestingly, on my Windows test machine (Windows 7)
> I don't get these warnings (R-devel from 2018-01-07 r74091).
>
> jo
>
> > On 16 Apr 2018, at 10:49, Mike Smith  wrote:
> >
> > Hi Johannes,
> >
> > xcms is certainly not alone with the warning, and it was discussed in
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> >
> > I think you should be able to get round it by including the name of Rd
> file you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
> (I haven't actually tested this though).
> >
> > Mike
> >
> > On 16 April 2018 at 09:06, Rainer Johannes 
> wrote:
> > Dear all,
> >
> > we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> > Example:
> > we have \code{\link[MSnbase]{pickPeaks}} in
> XCMSnExp-inherited-methods.Rd that links to the method in MSnbase, that
> works nicely on Linux and macOS build machines, but on tokay2 we get:
> >
> >   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
> >
> > is there any other solution to removing all links to external packages?
> >
> > thanks, jo
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>

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Re: [Bioc-devel] Windows

[Rainer Johannes]

Thanks Mike,

I somehow missed the discussion you mentioned. I would really not like to 
include the name of the Rd file I want to link to. The *default* way that works 
on Linux and macOS should also work on Windows - otherwise what's the matter of 
the alias? Interestingly, on my Windows test machine (Windows 7) I don't get 
these warnings (R-devel from 2018-01-07 r74091).

jo

> On 16 Apr 2018, at 10:49, Mike Smith  wrote:
> 
> Hi Johannes,
> 
> xcms is certainly not alone with the warning, and it was discussed in 
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
> 
> I think you should be able to get round it by including the name of Rd file 
> you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}} (I 
> haven't actually tested this though).
> 
> Mike
> 
> On 16 April 2018 at 09:06, Rainer Johannes  wrote:
> Dear all,
> 
> we're experiencing WARNINGS in xcms on Tokay2 that are all related to links 
> in Rd files to functions and methods in other packages.
> Example:
> we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd 
> that links to the method in MSnbase, that works nicely on Linux and macOS 
> build machines, but on tokay2 we get:
> 
>   Rd warning: 
> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59:
>  file link 'pickPeaks' in package 'MSnbase' does not exist and so has been 
> treated as a topic
> 
> is there any other solution to removing all links to external packages?
> 
> thanks, jo
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 

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Re: [Bioc-devel] Windows

[Mike Smith]

Hi Johannes,

xcms is certainly not alone with the warning, and it was discussed in
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html

I think you should be able to get round it by including the name of Rd file
you're linking to e.g.  \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
(I haven't actually tested this though).

Mike

On 16 April 2018 at 09:06, Rainer Johannes 
wrote:

> Dear all,
>
> we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> Example:
> we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd
> that links to the method in MSnbase, that works nicely on Linux and macOS
> build machines, but on tokay2 we get:
>
>   Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
>
> is there any other solution to removing all links to external packages?
>
> thanks, jo
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] Windows

[Rainer Johannes]

Dear all,

we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in 
Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that 
links to the method in MSnbase, that works nicely on Linux and macOS build 
machines, but on tokay2 we get:

  Rd warning: 
C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59:
 file link 'pickPeaks' in package 'MSnbase' does not exist and so has been 
treated as a topic

is there any other solution to removing all links to external packages?

thanks, jo

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[Bioc-devel] Windows devel builds: NAs in BUILD BIN

[Obenchain, Valerie]

Hi,

You may have noticed occasional 'NA' values in the 'BUILD BIN' column on the 
the Windows (tokay2) build report. These NAs appear when the build products 
from the nodes (Windows and Mac) are not available to the postrun script on 
master (Linux). This 'unavailability' can be due to network connectivity 
problems or a problem with the individual node.

tokay2 is not as powerful as the Mac and Linux builders. As more packages are 
added to the repository tokay2 has been inching closer to the max build time. 
Building binaries is the last step performed in tokay2's sequence and when it 
doesn't complete in time we see NAs in 'BUILD BIN' for all packages that did 
not make the postrun cutoff.

Over the next week Herve will be making some changes to the build sequence that 
will reduce the number of times each package is installed. This will reduce 
build times across all builders and tokay2 should once again complete well 
before the postrun starts.

In the meantime, please ignore the NAs on the Windows report.

Thanks.
Valerie


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Re: [Bioc-devel] Windows binaries for the new release?

[James W. MacDonald]

On Wed, Apr 26, 2017 at 11:26 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 04/26/2017 11:23 AM, James W. MacDonald wrote:
>
>>
>>
>> On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan
>> >
>> wrote:
>>
>> On 04/26/2017 10:34 AM, James W. MacDonald wrote:
>>
>>
>>
>> On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan
>> > 
>> >
>> >>
>>
>> wrote:
>>
>> On 04/26/2017 10:00 AM, James W. MacDonald wrote:
>>
>> I see the binaries on the respective web pages, but
>> biocLite
>> seems not to:
>>
>>
>> I'm not 100% sure but can you try again in a new R session?
>> I think
>> you have a cached version of the repository index.
>>
>>
>> At a command prompt, using --vanilla:
>>
>> C:\Users\jmacdon> C:\Progra~1\R\R-3.4.0\bin\x64\R --vanilla
>>
>> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>>   Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>> library(BiocInstaller)
>>
>> Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for
>> help
>>
>> biocLite()
>>
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0
>> (2017-04-21).
>> installation path not writeable, unable to update packages:
>> foreign
>> Old packages: 'Biobase', 'IRanges', 'S4Vectors'
>> Update all/some/none? [a/s/n]: a
>>
>>   There are binary versions available but the source versions
>> are later:
>>binary source needs_compilation
>> Biobase2.35.1 2.36.0  TRUE
>> IRanges2.9.19 2.10.0  TRUE
>> S4Vectors 0.13.17 0.14.0  TRUE
>>
>> Do you want to install from sources the packages which need
>> compilation?
>> y/n:
>>
>> Is there a way to remove the cache manually? I have already
>> uninstalled
>> and re-installed BiocInstaller.
>>
>>
>>   contrib.url(BiocInstaller::biocinstallRepos())
>>
>> should be pointing to
>>
>>   https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib
>> 
>>
>> and
>>
>>   https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib
>> 
>> /3.4/PACKAGES
>>
>> has the current information
>>
>> Package: Biobase
>> Version: 2.36.0
>> Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils
>> Imports: methods
>> Suggests: tools, tkWidgets, ALL, RUnit, golubEsets
>> License: Artistic-2.0
>> Archs: i386, x64
>>
>> as well as in R
>>
>> > fl =
>> "https://bioconductor.org/packages/3.5/bioc/bin/windows/cont
>> rib/3.4/PACKAGES.rds
>> > rib/3.4/PACKAGES.rds>"
>> > xx = readRDS(url(fl))
>> > xx['Biobase', , drop=FALSE]Package   Version  Priority
>> Biobase "Biobase" "2.36.0" NA
>> Depends   Imports
>>  LinkingTo
>> Biobase "R (>= 2.10), BiocGenerics (>= 0.3.2), utils" "methods" NA
>> Suggests   Enhances License
>> Biobase "tools, tkWidgets, ALL, RUnit, golubEsets" NA
>>  "Artistic-2.0"
>> License_is_FOSS License_restricts_use OS_type Archs
>>  MD5sum
>> Biobase NA  NANA  "i386, x64" NA
>>
>> should be pointing to the current .zip files.
>>
>> biocLite() delegates to available.packages(), which should be
>> checking the session temporary directory and, since you're in a new
>> session, retrieving the rds file above. You could
>>
>>   debug(available.packages)
>>
>> and try and figure out where the issue is?
>>
>> FWIW with a new R installation I could not reproduce your problem.
>>
>>
>> OK. If 

Re: [Bioc-devel] Windows binaries for the new release?

[Martin Morgan]

On 04/26/2017 11:23 AM, James W. MacDonald wrote:



On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan
>
wrote:

On 04/26/2017 10:34 AM, James W. MacDonald wrote:



On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan

>>

wrote:

On 04/26/2017 10:00 AM, James W. MacDonald wrote:

I see the binaries on the respective web pages, but biocLite
seems not to:


I'm not 100% sure but can you try again in a new R session?
I think
you have a cached version of the repository index.


At a command prompt, using --vanilla:

C:\Users\jmacdon> C:\Progra~1\R\R-3.4.0\bin\x64\R --vanilla

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

library(BiocInstaller)

Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help

biocLite()

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
installation path not writeable, unable to update packages: foreign
Old packages: 'Biobase', 'IRanges', 'S4Vectors'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions
are later:
   binary source needs_compilation
Biobase2.35.1 2.36.0  TRUE
IRanges2.9.19 2.10.0  TRUE
S4Vectors 0.13.17 0.14.0  TRUE

Do you want to install from sources the packages which need
compilation?
y/n:

Is there a way to remove the cache manually? I have already
uninstalled
and re-installed BiocInstaller.


  contrib.url(BiocInstaller::biocinstallRepos())

should be pointing to

  https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib


and

  https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib

/3.4/PACKAGES

has the current information

Package: Biobase
Version: 2.36.0
Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils
Imports: methods
Suggests: tools, tkWidgets, ALL, RUnit, golubEsets
License: Artistic-2.0
Archs: i386, x64

as well as in R

> fl =

"https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/PACKAGES.rds

"
> xx = readRDS(url(fl))
> xx['Biobase', , drop=FALSE]Package   Version  Priority
Biobase "Biobase" "2.36.0" NA
Depends   Imports
 LinkingTo
Biobase "R (>= 2.10), BiocGenerics (>= 0.3.2), utils" "methods" NA
Suggests   Enhances License
Biobase "tools, tkWidgets, ALL, RUnit, golubEsets" NA
 "Artistic-2.0"
License_is_FOSS License_restricts_use OS_type Archs   MD5sum
Biobase NA  NANA  "i386, x64" NA

should be pointing to the current .zip files.

biocLite() delegates to available.packages(), which should be
checking the session temporary directory and, since you're in a new
session, retrieving the rds file above. You could

  debug(available.packages)

and try and figure out where the issue is?

FWIW with a new R installation I could not reproduce your problem.


OK. If it's just weirdness on my end I don't really care. I was just
concerned that this would be a problem for regular end users.


If you're having a problem then it would be great to have your expert 
insight into what is going wrong...


Martin



Thanks,

Jim





> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)

Matrix products: default

locale:

Re: [Bioc-devel] Windows binaries for the new release?

[James W. MacDonald]

On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 04/26/2017 10:34 AM, James W. MacDonald wrote:
>
>>
>>
>> On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan
>> >
>>
>> wrote:
>>
>> On 04/26/2017 10:00 AM, James W. MacDonald wrote:
>>
>> I see the binaries on the respective web pages, but biocLite
>> seems not to:
>>
>>
>> I'm not 100% sure but can you try again in a new R session? I think
>> you have a cached version of the repository index.
>>
>>
>> At a command prompt, using --vanilla:
>>
>> C:\Users\jmacdon> C:\Progra~1\R\R-3.4.0\bin\x64\R --vanilla
>>
>> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>>   Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>> library(BiocInstaller)
>>>
>> Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
>>
>>> biocLite()
>>>
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
>> installation path not writeable, unable to update packages: foreign
>> Old packages: 'Biobase', 'IRanges', 'S4Vectors'
>> Update all/some/none? [a/s/n]: a
>>
>>   There are binary versions available but the source versions are later:
>>binary source needs_compilation
>> Biobase2.35.1 2.36.0  TRUE
>> IRanges2.9.19 2.10.0  TRUE
>> S4Vectors 0.13.17 0.14.0  TRUE
>>
>> Do you want to install from sources the packages which need compilation?
>> y/n:
>>
>> Is there a way to remove the cache manually? I have already uninstalled
>> and re-installed BiocInstaller.
>>
>
>   contrib.url(BiocInstaller::biocinstallRepos())
>
> should be pointing to
>
>   https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib
>
> and
>
>   https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib
> /3.4/PACKAGES
>
> has the current information
>
> Package: Biobase
> Version: 2.36.0
> Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils
> Imports: methods
> Suggests: tools, tkWidgets, ALL, RUnit, golubEsets
> License: Artistic-2.0
> Archs: i386, x64
>
> as well as in R
>
> > fl = "https://bioconductor.org/packages/3.5/bioc/bin/windows/cont
> rib/3.4/PACKAGES.rds"
> > xx = readRDS(url(fl))
> > xx['Biobase', , drop=FALSE]Package   Version  Priority
> Biobase "Biobase" "2.36.0" NA
> Depends   Imports   LinkingTo
> Biobase "R (>= 2.10), BiocGenerics (>= 0.3.2), utils" "methods" NA
> Suggests   Enhances License
> Biobase "tools, tkWidgets, ALL, RUnit, golubEsets" NA   "Artistic-2.0"
> License_is_FOSS License_restricts_use OS_type Archs   MD5sum
> Biobase NA  NANA  "i386, x64" NA
>
> should be pointing to the current .zip files.
>
> biocLite() delegates to available.packages(), which should be checking the
> session temporary directory and, since you're in a new session, retrieving
> the rds file above. You could
>
>   debug(available.packages)
>
> and try and figure out where the issue is?
>
> FWIW with a new R installation I could not reproduce your problem.


OK. If it's just weirdness on my end I don't really care. I was just
concerned that this would be a problem for regular end users.

Thanks,

Jim



>
>
> > sessionInfo()
> R version 3.4.0 (2017-04-21)
> Platform: i386-w64-mingw32/i386 (32-bit)
> Running under: Windows Server 2012 R2 x64 (build 9600)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.26.0
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0 tools_3.4.0
>
> Martin
>
>
>
>> Jim
>>
>>
>>
>>
>> Martin
>>
>>
>> biocLite()
>>
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0
>> (2017-04-21).
>> installation path not writeable, unable to update packages:
>> foreign
>> Old packages: 'AnnotationDbi', 'Biobase', 'BiocGenerics',
>> 

Re: [Bioc-devel] Windows binaries for the new release?

[Martin Morgan]

On 04/26/2017 10:34 AM, James W. MacDonald wrote:



On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan
>
wrote:

On 04/26/2017 10:00 AM, James W. MacDonald wrote:

I see the binaries on the respective web pages, but biocLite
seems not to:


I'm not 100% sure but can you try again in a new R session? I think
you have a cached version of the repository index.


At a command prompt, using --vanilla:

C:\Users\jmacdon> C:\Progra~1\R\R-3.4.0\bin\x64\R --vanilla

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


library(BiocInstaller)

Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help

biocLite()

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
installation path not writeable, unable to update packages: foreign
Old packages: 'Biobase', 'IRanges', 'S4Vectors'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions are later:
   binary source needs_compilation
Biobase2.35.1 2.36.0  TRUE
IRanges2.9.19 2.10.0  TRUE
S4Vectors 0.13.17 0.14.0  TRUE

Do you want to install from sources the packages which need compilation?
y/n:

Is there a way to remove the cache manually? I have already uninstalled
and re-installed BiocInstaller.


  contrib.url(BiocInstaller::biocinstallRepos())

should be pointing to

  https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib

and

  https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib
/3.4/PACKAGES

has the current information

Package: Biobase
Version: 2.36.0
Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils
Imports: methods
Suggests: tools, tkWidgets, ALL, RUnit, golubEsets
License: Artistic-2.0
Archs: i386, x64

as well as in R

> fl = 
"https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/PACKAGES.rds;

> xx = readRDS(url(fl))
> xx['Biobase', , drop=FALSE]Package   Version  Priority
Biobase "Biobase" "2.36.0" NA
Depends   Imports   LinkingTo
Biobase "R (>= 2.10), BiocGenerics (>= 0.3.2), utils" "methods" NA
Suggests   Enhances License
Biobase "tools, tkWidgets, ALL, RUnit, golubEsets" NA   "Artistic-2.0"
License_is_FOSS License_restricts_use OS_type Archs   MD5sum
Biobase NA  NANA  "i386, x64" NA

should be pointing to the current .zip files.

biocLite() delegates to available.packages(), which should be checking 
the session temporary directory and, since you're in a new session, 
retrieving the rds file above. You could


  debug(available.packages)

and try and figure out where the issue is?

FWIW with a new R installation I could not reproduce your problem.

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] BiocInstaller_1.26.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0

Martin



Jim




Martin


biocLite()

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
installation path not writeable, unable to update packages: foreign
Old packages: 'AnnotationDbi', 'Biobase', 'BiocGenerics', 'biomaRt',
'IRanges',
  'S4Vectors'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions
are later:
   binary source needs_compilation
AnnotationDbi  1.37.4 1.38.0 FALSE
Biobase2.35.1 2.36.0  TRUE
BiocGenerics   0.21.3 0.22.0 FALSE
biomaRt   2.31.10 2.32.0 FALSE
IRanges2.9.19 2.10.0  TRUE
S4Vectors 0.13.17 0.14.0  TRUE

Re: [Bioc-devel] Windows binaries for the new release?

[James W. MacDonald]

On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:

> On 04/26/2017 10:00 AM, James W. MacDonald wrote:
>
>> I see the binaries on the respective web pages, but biocLite seems not to:
>>
>
> I'm not 100% sure but can you try again in a new R session? I think you
> have a cached version of the repository index.
>

At a command prompt, using --vanilla:

C:\Users\jmacdon> C:\Progra~1\R\R-3.4.0\bin\x64\R --vanilla

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BiocInstaller)
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
installation path not writeable, unable to update packages: foreign
Old packages: 'Biobase', 'IRanges', 'S4Vectors'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions are later:
   binary source needs_compilation
Biobase2.35.1 2.36.0  TRUE
IRanges2.9.19 2.10.0  TRUE
S4Vectors 0.13.17 0.14.0  TRUE

Do you want to install from sources the packages which need compilation?
y/n:

Is there a way to remove the cache manually? I have already uninstalled and
re-installed BiocInstaller.

Jim




> Martin
>
>
>> biocLite()
>>>
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
>> installation path not writeable, unable to update packages: foreign
>> Old packages: 'AnnotationDbi', 'Biobase', 'BiocGenerics', 'biomaRt',
>> 'IRanges',
>>   'S4Vectors'
>> Update all/some/none? [a/s/n]: a
>>
>>   There are binary versions available but the source versions are later:
>>binary source needs_compilation
>> AnnotationDbi  1.37.4 1.38.0 FALSE
>> Biobase2.35.1 2.36.0  TRUE
>> BiocGenerics   0.21.3 0.22.0 FALSE
>> biomaRt   2.31.10 2.32.0 FALSE
>> IRanges2.9.19 2.10.0  TRUE
>> S4Vectors 0.13.17 0.14.0  TRUE
>>
>> Do you want to install from sources the packages which need compilation?
>> y/n:
>>
>> sessionInfo()
>>>
>> R version 3.4.0 (2017-04-21)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 14393)
>>
>> Matrix products: default
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>>
>> other attached packages:
>> [1] BiocInstaller_1.26.0
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.4.0 tools_3.4.0
>>
>>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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Re: [Bioc-devel] Windows binaries for the new release?

[Martin Morgan]

On 04/26/2017 10:00 AM, James W. MacDonald wrote:

I see the binaries on the respective web pages, but biocLite seems not to:


I'm not 100% sure but can you try again in a new R session? I think you 
have a cached version of the repository index.


Martin




biocLite()

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
installation path not writeable, unable to update packages: foreign
Old packages: 'AnnotationDbi', 'Biobase', 'BiocGenerics', 'biomaRt',
'IRanges',
  'S4Vectors'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions are later:
   binary source needs_compilation
AnnotationDbi  1.37.4 1.38.0 FALSE
Biobase2.35.1 2.36.0  TRUE
BiocGenerics   0.21.3 0.22.0 FALSE
biomaRt   2.31.10 2.32.0 FALSE
IRanges2.9.19 2.10.0  TRUE
S4Vectors 0.13.17 0.14.0  TRUE

Do you want to install from sources the packages which need compilation?
y/n:


sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] BiocInstaller_1.26.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0




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[Bioc-devel] Windows binaries for the new release?

[James W. MacDonald]

I see the binaries on the respective web pages, but biocLite seems not to:

> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
installation path not writeable, unable to update packages: foreign
Old packages: 'AnnotationDbi', 'Biobase', 'BiocGenerics', 'biomaRt',
'IRanges',
  'S4Vectors'
Update all/some/none? [a/s/n]: a

  There are binary versions available but the source versions are later:
   binary source needs_compilation
AnnotationDbi  1.37.4 1.38.0 FALSE
Biobase2.35.1 2.36.0  TRUE
BiocGenerics   0.21.3 0.22.0 FALSE
biomaRt   2.31.10 2.32.0 FALSE
IRanges2.9.19 2.10.0  TRUE
S4Vectors 0.13.17 0.14.0  TRUE

Do you want to install from sources the packages which need compilation?
y/n:

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] BiocInstaller_1.26.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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Re: [Bioc-devel] Windows build error for outdated Shiny package

[Chen Hao]

Dear Martin,

Thanks very much.

Best Regards,
Chen Hao

> On 24 Sep 2016, at 5:44 PM, Martin Morgan  
> wrote:
> 
> On 09/24/2016 05:43 AM, Nuno Agostinho wrote:
>> Good evening,
>> 
>> I recently submitted a package to Bioconductor. Unfortunately, the Windows 
>> machine (moscato1) returned the following error while building the package: 
>> Error : package 'shiny' 0.13.2 was found, but >= 0.14 is required by 
>> 'psichomics'
>> 
>> The issue related to the package in question is 
>> https://github.com/Bioconductor/Contributions/issues/139
>> 
>> I require version 0.14 for some of the features it introduced. What can I do 
>> to fix this error?
>> Thanks in advance.
> 
> you can't do anything; it will be addressed on our end. You and your 
> reviewer can ignore it for now.
> 
> Martin
> 
>> 
>> Best regards,
>> Nuno Agostinho
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> 
> This email message may contain legally privileged and/or...{{dropped:2}}
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Windows build error for outdated Shiny package

[Martin Morgan]

On 09/24/2016 05:43 AM, Nuno Agostinho wrote:

Good evening,

I recently submitted a package to Bioconductor. Unfortunately, the Windows machine 
(moscato1) returned the following error while building the package: Error : 
package 'shiny' 0.13.2 was found, but >= 0.14 is required by 'psichomics'

The issue related to the package in question is 
https://github.com/Bioconductor/Contributions/issues/139

I require version 0.14 for some of the features it introduced. What can I do to 
fix this error?
Thanks in advance.


you can't do anything; it will be addressed on our end. You and your 
reviewer can ignore it for now.


Martin



Best regards,
Nuno Agostinho

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[Bioc-devel] Windows build error for outdated Shiny package

[Nuno Agostinho]

Good evening,

I recently submitted a package to Bioconductor. Unfortunately, the Windows 
machine (moscato1) returned the following error while building the package: 
Error : package 'shiny' 0.13.2 was found, but >= 0.14 is required by 
'psichomics'

The issue related to the package in question is 
https://github.com/Bioconductor/Contributions/issues/139

I require version 0.14 for some of the features it introduced. What can I do to 
fix this error?
Thanks in advance.

Best regards,
Nuno Agostinho

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Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

[Leonardo Collado Torres]

Thanks Martin! Using mode='wb' solved the issue.

On Sat, Jun 18, 2016 at 10:41 AM, Martin Morgan
 wrote:
> On 06/18/2016 12:58 AM, Leonardo Collado Torres wrote:
>>
>> Hi,
>>
>> I get the same error while hosting the data somewhere else or when using
>> RawGit's url. That is:
>>
>>> library('downloader')
>>> download('
>>
>> http://www.biostat.jhsph.edu/~lcollado/recount/metadata_clean_sra.Rdata',
>> destfile = 'test2.Rdata')
>>>
>>> load('tes2t.Rdata')
>>
>> Error: ReadItem: unknown type 50, perhaps written by later version of R
>>>
>>> download('
>>
>>
>> https://cdn.rawgit.com/leekgroup/recount-website/master/metadata/metadata_clean_sra.Rdata',
>> destfile = 'test3.Rdata')
>>>
>>> load('test3.Rdata')
>>
>> Error: ReadItem: unknown type 50, perhaps written by later version of R
>>
>> Again, it only happens on Windows but not on the other OS. So it doesn't
>> look like a GitHub issue.
>
>
> use mode="wb" to download in binary mode.
>
> Martin
>
>>
>> Best,
>> Leo
>>
>>
>> On Fri, Jun 17, 2016 at 4:57 PM, Gabe Becker  wrote:
>>
>>> I wonder if raw only means "raw after line return munging"? can you
>>> attach
>>> the file that gets downloaded  via email? (off list is fine)
>>>
>>> On Fri, Jun 17, 2016 at 1:44 PM, Leonardo Collado Torres
>>> >>
>>>
 Hi,

 I'm trying to figure out what is going wrong with an error that pops
 up on Windows only. It's currently the only error for a package that I
 recently submitted to Bioc. The function is fairly simple: it
 downloads a Rdata file from the web and loads it.

 If I try to download and load the file with R, the following error
 occurs (only on Windows):


> library('downloader')
> download('


 https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true',
 destfile = 'test.Rdata')
 trying URL '

 https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true
 '
 Content type 'application/octet-stream' length 2531337 bytes (2.4 MB)
 downloaded 2.4 MB

> load('test.Rdata')

 Error: ReadItem: unknown type 50, perhaps written by later version of R
>
> traceback()

 1: load("test.Rdata")
>
> options(width = 120)
> devtools::session_info()

 Session info

 ---
   setting  value
   version  R version 3.3.0 (2016-05-03)
   system   x86_64, mingw32
   ui   Rgui
   language (EN)
   collate  English_United States.1252
   tz   America/New_York
   date 2016-06-17

 Packages

 ---
   package* version date   source
   devtools 1.11.1  2016-04-21 CRAN (R 3.3.0)
   digest   0.6.9   2016-01-08 CRAN (R 3.3.0)
   downloader * 0.4 2015-07-09 CRAN (R 3.3.0)
   memoise  1.0.0   2016-01-29 CRAN (R 3.3.0)
   withr1.0.1   2016-02-04 CRAN (R 3.3.0)
>
>


 If I open the same url on my browser and manually download the file,
 then everything works as shown below:

> load('metadata_clean_sra.Rdata')
> metadata_clean

 Loading required package: S4Vectors
 Loading required package: stats4
 Loading required package: BiocGenerics
 Loading required package: parallel
 ## removed more output

> options(width = 120)
> devtools::session_info()

 Session info

 ---
   setting  value
   version  R version 3.3.0 (2016-05-03)
   system   x86_64, mingw32
   ui   Rgui
   language (EN)
   collate  English_United States.1252
   tz   America/New_York
   date 2016-06-17

 Packages

 ---
   package  * version date   source
   BiocGenerics * 0.19.1  2016-06-17 Bioconductor
   devtools   1.11.1  2016-04-21 CRAN (R 3.3.0)
   digest 0.6.9   2016-01-08 CRAN (R 3.3.0)
   IRanges  * 2.7.2   2016-06-07 Bioconductor
   memoise1.0.0   2016-01-29 CRAN (R 3.3.0)
   S4Vectors* 0.11.3  2016-06-03 Bioconductor
   withr  1.0.1   2016-02-04 CRAN (R 3.3.0)
>
> print(object.size(metadata_clean), units = 'Mb')

 30.5 Mb

 The object itself is a DataFrame and was created using R 3.3.1 with
 S4Vectors version 0.11.4. I get the same error if using a Unix machine
 I re-save the data using R 3.3.0 (with S4Vectors from Bioc-release).

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

[Martin Morgan]

On 06/18/2016 12:58 AM, Leonardo Collado Torres wrote:

Hi,

I get the same error while hosting the data somewhere else or when using
RawGit's url. That is:


library('downloader')
download('

http://www.biostat.jhsph.edu/~lcollado/recount/metadata_clean_sra.Rdata',
destfile = 'test2.Rdata')

load('tes2t.Rdata')

Error: ReadItem: unknown type 50, perhaps written by later version of R

download('

https://cdn.rawgit.com/leekgroup/recount-website/master/metadata/metadata_clean_sra.Rdata',
destfile = 'test3.Rdata')

load('test3.Rdata')

Error: ReadItem: unknown type 50, perhaps written by later version of R

Again, it only happens on Windows but not on the other OS. So it doesn't
look like a GitHub issue.


use mode="wb" to download in binary mode.

Martin



Best,
Leo


On Fri, Jun 17, 2016 at 4:57 PM, Gabe Becker  wrote:


I wonder if raw only means "raw after line return munging"? can you attach
the file that gets downloaded  via email? (off list is fine)

On Fri, Jun 17, 2016 at 1:44 PM, Leonardo Collado Torres 

Re: [Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

[Leonardo Collado Torres]

Hi,

I get the same error while hosting the data somewhere else or when using
RawGit's url. That is:

> library('downloader')
> download('
http://www.biostat.jhsph.edu/~lcollado/recount/metadata_clean_sra.Rdata',
destfile = 'test2.Rdata')
> load('tes2t.Rdata')
Error: ReadItem: unknown type 50, perhaps written by later version of R
> download('
https://cdn.rawgit.com/leekgroup/recount-website/master/metadata/metadata_clean_sra.Rdata',
destfile = 'test3.Rdata')
> load('test3.Rdata')
Error: ReadItem: unknown type 50, perhaps written by later version of R

Again, it only happens on Windows but not on the other OS. So it doesn't
look like a GitHub issue.

Best,
Leo


On Fri, Jun 17, 2016 at 4:57 PM, Gabe Becker  wrote:

> I wonder if raw only means "raw after line return munging"? can you attach
> the file that gets downloaded  via email? (off list is fine)
>
> On Fri, Jun 17, 2016 at 1:44 PM, Leonardo Collado Torres  > wrote:
>
>> Hi,
>>
>> I'm trying to figure out what is going wrong with an error that pops
>> up on Windows only. It's currently the only error for a package that I
>> recently submitted to Bioc. The function is fairly simple: it
>> downloads a Rdata file from the web and loads it.
>>
>> If I try to download and load the file with R, the following error
>> occurs (only on Windows):
>>
>>
>> > library('downloader')
>> > download('
>> https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true',
>> destfile = 'test.Rdata')
>> trying URL '
>> https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true
>> '
>> Content type 'application/octet-stream' length 2531337 bytes (2.4 MB)
>> downloaded 2.4 MB
>>
>> > load('test.Rdata')
>> Error: ReadItem: unknown type 50, perhaps written by later version of R
>> > traceback()
>> 1: load("test.Rdata")
>> > options(width = 120)
>> > devtools::session_info()
>> Session info
>> ---
>>  setting  value
>>  version  R version 3.3.0 (2016-05-03)
>>  system   x86_64, mingw32
>>  ui   Rgui
>>  language (EN)
>>  collate  English_United States.1252
>>  tz   America/New_York
>>  date 2016-06-17
>>
>> Packages
>> ---
>>  package* version date   source
>>  devtools 1.11.1  2016-04-21 CRAN (R 3.3.0)
>>  digest   0.6.9   2016-01-08 CRAN (R 3.3.0)
>>  downloader * 0.4 2015-07-09 CRAN (R 3.3.0)
>>  memoise  1.0.0   2016-01-29 CRAN (R 3.3.0)
>>  withr1.0.1   2016-02-04 CRAN (R 3.3.0)
>> >
>>
>>
>> If I open the same url on my browser and manually download the file,
>> then everything works as shown below:
>>
>> > load('metadata_clean_sra.Rdata')
>> > metadata_clean
>> Loading required package: S4Vectors
>> Loading required package: stats4
>> Loading required package: BiocGenerics
>> Loading required package: parallel
>> ## removed more output
>>
>> > options(width = 120)
>> > devtools::session_info()
>> Session info
>> ---
>>  setting  value
>>  version  R version 3.3.0 (2016-05-03)
>>  system   x86_64, mingw32
>>  ui   Rgui
>>  language (EN)
>>  collate  English_United States.1252
>>  tz   America/New_York
>>  date 2016-06-17
>>
>> Packages
>> ---
>>  package  * version date   source
>>  BiocGenerics * 0.19.1  2016-06-17 Bioconductor
>>  devtools   1.11.1  2016-04-21 CRAN (R 3.3.0)
>>  digest 0.6.9   2016-01-08 CRAN (R 3.3.0)
>>  IRanges  * 2.7.2   2016-06-07 Bioconductor
>>  memoise1.0.0   2016-01-29 CRAN (R 3.3.0)
>>  S4Vectors* 0.11.3  2016-06-03 Bioconductor
>>  withr  1.0.1   2016-02-04 CRAN (R 3.3.0)
>> > print(object.size(metadata_clean), units = 'Mb')
>> 30.5 Mb
>>
>> The object itself is a DataFrame and was created using R 3.3.1 with
>> S4Vectors version 0.11.4. I get the same error if using a Unix machine
>> I re-save the data using R 3.3.0 (with S4Vectors from Bioc-release).
>>
>> Some google leads are "corrupt file" or something about a hidden
>> session Rdata file. But from the manual test, everything looks line.
>> Unless downloader::download() (or alternatively utils::download.file()
>> ) is corrupting the file.
>>
>>
>> An option would be to include the data in the package, but I'd like to
>> avoid doing so to minimize the package size. It already has a big
>> data.frame that is necessary for the package to work. This short
>> function is there for convenience.
>>
>> Best,
>> Leo
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>

[Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

[Leonardo Collado Torres]

Hi,

I'm trying to figure out what is going wrong with an error that pops
up on Windows only. It's currently the only error for a package that I
recently submitted to Bioc. The function is fairly simple: it
downloads a Rdata file from the web and loads it.

If I try to download and load the file with R, the following error
occurs (only on Windows):


> library('downloader')
> download('https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true',
>  destfile = 'test.Rdata')
trying URL 
'https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true'
Content type 'application/octet-stream' length 2531337 bytes (2.4 MB)
downloaded 2.4 MB

> load('test.Rdata')
Error: ReadItem: unknown type 50, perhaps written by later version of R
> traceback()
1: load("test.Rdata")
> options(width = 120)
> devtools::session_info()
Session info 
---
 setting  value
 version  R version 3.3.0 (2016-05-03)
 system   x86_64, mingw32
 ui   Rgui
 language (EN)
 collate  English_United States.1252
 tz   America/New_York
 date 2016-06-17

Packages 
---
 package* version date   source
 devtools 1.11.1  2016-04-21 CRAN (R 3.3.0)
 digest   0.6.9   2016-01-08 CRAN (R 3.3.0)
 downloader * 0.4 2015-07-09 CRAN (R 3.3.0)
 memoise  1.0.0   2016-01-29 CRAN (R 3.3.0)
 withr1.0.1   2016-02-04 CRAN (R 3.3.0)
>


If I open the same url on my browser and manually download the file,
then everything works as shown below:

> load('metadata_clean_sra.Rdata')
> metadata_clean
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
## removed more output

> options(width = 120)
> devtools::session_info()
Session info 
---
 setting  value
 version  R version 3.3.0 (2016-05-03)
 system   x86_64, mingw32
 ui   Rgui
 language (EN)
 collate  English_United States.1252
 tz   America/New_York
 date 2016-06-17

Packages 
---
 package  * version date   source
 BiocGenerics * 0.19.1  2016-06-17 Bioconductor
 devtools   1.11.1  2016-04-21 CRAN (R 3.3.0)
 digest 0.6.9   2016-01-08 CRAN (R 3.3.0)
 IRanges  * 2.7.2   2016-06-07 Bioconductor
 memoise1.0.0   2016-01-29 CRAN (R 3.3.0)
 S4Vectors* 0.11.3  2016-06-03 Bioconductor
 withr  1.0.1   2016-02-04 CRAN (R 3.3.0)
> print(object.size(metadata_clean), units = 'Mb')
30.5 Mb

The object itself is a DataFrame and was created using R 3.3.1 with
S4Vectors version 0.11.4. I get the same error if using a Unix machine
I re-save the data using R 3.3.0 (with S4Vectors from Bioc-release).

Some google leads are "corrupt file" or something about a hidden
session Rdata file. But from the manual test, everything looks line.
Unless downloader::download() (or alternatively utils::download.file()
) is corrupting the file.


An option would be to include the data in the package, but I'd like to
avoid doing so to minimize the package size. It already has a big
data.frame that is necessary for the package to work. This short
function is there for convenience.

Best,
Leo

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[Bioc-devel] Windows build error: cannot open file 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpaEUpE0\xshell23645160444e': Permission denied

[Coetzee, Simon G]

I am working on getting a package ready for Bioconductor called motifbreakR.

http://bioconductor.org/spb_reports/motifbreakR_0.99.7_buildreport_20150818123558.html#moscato1_buildsrc_anchor

This is the build report. My package has as part of it’s plotting function, the 
necessity of producing a temporary file that is read back in. This is likely 
where the issue lies, but I’m not entirely sure about the build environment, 
and where exactly the permissions issue lies. I am able produce the package on 
a local windows install; this includes the generation of the vignette during 
the build.

Thanks for looking at this.

Simon Gert Coetzee
Research Biostatistician
Department of Biomedical Sciences
––
Cedars-Sinai Medical Center
Advanced Health Sciences Pavilion 8th Floor
127 S. San Vicente Blvd.
Los Angles, CA 90048

☎️ Phone: 424.315.2651
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