Re: [Bioc-devel] xps build problem on veracruz2

[Dan Tenenbaum]

Disabling SIP should not be done anywhere. Every page I've read on this topic 
strongly discourages doing this.


- Original Message -
> From: "Hervé Pagès" 
> To: "cstrato" , "Dan Tenenbaum" 
> Cc: "bioc-devel" 
> Sent: Thursday, April 20, 2017 3:17:23 PM
> Subject: Re: [Bioc-devel] xps build problem on veracruz2

> On 04/20/2017 03:01 PM, cstrato wrote:
>> Dear Herve,
>>
>> Doing 'csrutil disable' does indeed solve the problem, since:
>>
>> 1, in this way I was able to build xps on Mac OS Sierra
>>
>> 2, in this way I could already help one user of xps, see:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=
>>
>> This means, that users of xps seem to be willing to disable csrutil.
> 
> I'm not a statistician but I wouldn't draw conclusions from a sample
> of size 1. Mac users who cannot install xps on their machine will
> use something else, or, if they desperately need xps, they will
> grab a Linux box.
> 
> Sorry but disabling SIP on our Mac builders is not an option.
> 
>>
>>
>>
>> However, I just realized that there may be an even greater problem,
>> namely, which version of ROOT should a user install?
>>
>> People can download ROOT binaries built with XCode 7.x from:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=
>> for OS X 10.10 and 10.11.
>>
>> Thus for El Capitan they can download the following binaries:
>> - root_v5.34.36.macosx64-10.11-clang70.dmg
>> - root_v5.34.36.macosx64-10.11-clang70.tar.gz
>>
>> Did you install one of those binaries or did you compile ROOT from source?
> 
> As I said earlier, I compiled ROOT 5 from source on veracruz2.
> 
>>
>> With the help of my README file people could compile ROOT from source
>> for XCode 8.x.
>>
>>
>> However, you have mentioned that the CRAN people are using clang 4.0.0
>> for producing the Mac binaries of R and CRAN packages and thus you are
>> using the same on veracruz2.
> 
> Yes.
> 
>>
>> Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which
>> is not officially supported by Apple?
> 
> With clang 4.0.0.
> 
>>
>> The question is whether xps built with this version of ROOT will work
>> with the ROOT binaries which people can download from ROOT?
> 
> I guess someone will need to figure this out.
> 
> Note that if people need to compile their own ROOT anyway in order to
> be able to use the xps binary we distribute, then they should also be
> able to install xps from source. So that defeats the purpose of
> providing a binary in the first place.
> 
> Cheers,
> H.
> 
>>
>> Best regards,
>> Christian
>>
>>
>>
>> On 04/20/17 20:00, Hervé Pagès wrote:
>>> On 04/20/2017 10:59 AM, Hervé Pagès wrote:
 Hi Christian,

 Disabling 'csrutil disable' might help xps on veracruz2 but that
>>>   ^^
>>> oops, no double negative intended here. I meant, doing 'csrutil disable'
>>> might help... etc
>>>
>>> H.
>>>
 won't help your end users.

 I'm no expert in developing a package on Mac but other people on
 this list are. Also R-SIG-Mac might be a good place to seek help
 for this.

 Cheers,
 H.


 On 04/20/2017 10:53 AM, cstrato wrote:
> Dear Herve,
>
> Thank you for your efforts to try to install xps. I am glad to hear
> that
> you could build ROOT 5 from source.
>
> It's a pity that Apple does no longer allow the use of
> DYLD_LIBRARY_PATH. This seems to break the code of a lot of people
> (when
> googling around).
>
> I will try to change the build process and will see if I succeed.
> However, at the moment I have a couple of questions:
>
>
> 1, Is there any reason that you do not want to 'csrutil disable'?
>
>
> 2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
> 'configure.in' file, however, I have also to change the 'Makefile'.
>
> Since you say that the problem can be solved by adding the -rpath flag
> when linking, I assume that I have to change  the following line in my
> 'Makefile':
> $(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
>$(OutPutOpt) $(subst .$(DllSuf),.so,$@)
>
> Since I am not familiar with -rpath can you give me a hint how to
> change
> it?
>
>
> 3, There is a Wikipedia explanation for '-rpath', see:
> 

Re: [Bioc-devel] xps build problem on veracruz2

[Hervé Pagès]

Also relying on [DY]LD_LIBRARY_PATH is considered bad practice and
has been discouraged for years. xps is the only Bioconductor package
that relies on these variables for its configure/build process.

H.

On 04/20/2017 03:24 PM, Dan Tenenbaum wrote:

Disabling SIP should not be done anywhere. Every page I've read on this topic 
strongly discourages doing this.


- Original Message -

From: "Hervé Pagès" 
To: "cstrato" , "Dan Tenenbaum" 
Cc: "bioc-devel" 
Sent: Thursday, April 20, 2017 3:17:23 PM
Subject: Re: [Bioc-devel] xps build problem on veracruz2



On 04/20/2017 03:01 PM, cstrato wrote:

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=

This means, that users of xps seem to be willing to disable csrutil.


I'm not a statistician but I wouldn't draw conclusions from a sample
of size 1. Mac users who cannot install xps on their machine will
use something else, or, if they desperately need xps, they will
grab a Linux box.

Sorry but disabling SIP on our Mac builders is not an option.





However, I just realized that there may be an even greater problem,
namely, which version of ROOT should a user install?

People can download ROOT binaries built with XCode 7.x from:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=
for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT from source?


As I said earlier, I compiled ROOT 5 from source on veracruz2.



With the help of my README file people could compile ROOT from source
for XCode 8.x.


However, you have mentioned that the CRAN people are using clang 4.0.0
for producing the Mac binaries of R and CRAN packages and thus you are
using the same on veracruz2.


Yes.



Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which
is not officially supported by Apple?


With clang 4.0.0.



The question is whether xps built with this version of ROOT will work
with the ROOT binaries which people can download from ROOT?


I guess someone will need to figure this out.

Note that if people need to compile their own ROOT anyway in order to
be able to use the xps binary we distribute, then they should also be
able to install xps from source. So that defeats the purpose of
providing a binary in the first place.

Cheers,
H.



Best regards,
Christian



On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc

H.


won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.


On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear
that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people
(when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:


1, Is there any reason that you do not want to 'csrutil disable'?


2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since you say that the problem can be solved by adding the -rpath flag
when linking, I assume that I have to change  the following line in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint how to
change
it?


3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=




Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable 

Re: [Bioc-devel] Object not found in vignette

[王棣台]

Oh...
I think I forget to add...
Thanks a lot.

Ti-Tai


��: Michael Lawrence [lawrence.mich...@gene.com]
寄件日期: 2017年4月21日 上午 06:12
至: 王棣台
副本: Hervé Pagès; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Did you "svn add" the file?

On Thu, Apr 20, 2017 at 3:10 PM, 王棣台  wrote:
> I find that my data file will not change after I did any commit.
> That might be the problem.
> Is there anything I forget to do?
>
> Ti-Tai
> 
> ��: Hervé Pagès [hpa...@fredhutch.org]
> 寄件日期: 2017年4月21日 上午 06:00
> 至: 王棣台; bioc-devel@r-project.org
> 主旨: Re: [Bioc-devel] Object not found in vignette
>
> Also recently you bumped the version from 1.1.* to 1.2.*
> then went back to 1.1.* again. As a result the version that
> is available via biocLite() is 1.2.2, as reflected on the package
> landing page:
>
>https://bioconductor.org/packages/3.5/bioc/html/anamiR.html
>
> Any change you do to your package now won't propagate unless
> you bump the version to > 1.2.2.
>
> H.
>
> On 04/20/2017 02:52 PM, 王棣台 wrote:
>> it should be in my package since anamiR version 1.1.8
>> That is weird.
>>
>> Ti-Tai
>> 
>> ��: Hervé Pagès [hpa...@fredhutch.org]
>> 寄件日期: 2017年4月21日 上午 05:49
>> 至: 王棣台; bioc-devel@r-project.org
>> 主旨: Re: [Bioc-devel] Object not found in vignette
>>
>> On 04/20/2017 02:45 PM, Hervé Pagès wrote:
>>> On 04/20/2017 02:36 PM, 王棣台 wrote:
 That missing object is a list format data generated by myself,
 so I don't think it would be about Depends, Imports, or Suggests.
 Except this one, other generated data can be found.
>>>
>>> And where did you put this data set so that data(table_pre) can
>>> find it?
>>
>> I mean the other generated data sets can be found because they are
>> in your package but I don't see the table_pre data set there. Did you forget
>> to commit it?
>>
>> H.
>>
>>>
>>> H.
>>>

 Ti-Tai

 
 ��: Hervé Pagès [hpa...@fredhutch.org]
 寄件日期: 2017年4月21日 上午 05:16
 至: 王棣台; bioc-devel@r-project.org
 主旨: Re: [Bioc-devel] Object not found in vignette

 Why don't you give us the name of your package so we can look
 at it? I suspect something is missing in your Depends, Imports,
 or Suggests field. Works for you because you have the missing
 package installed on your machine but not on the build machine
 because the package is missing there. The build system (and your
 users) doesn't have this package so the vignette fails there.
 By adding the package to Depends, Imports, or Suggests, you let
 the build system know that this package needs to be installed
 before it tries to build the vignette.

 H.

 On 04/20/2017 01:51 PM, 王棣台 wrote:
> Hi all,
>
> I kept getting the same Error from BUILD REPORT:
>
>
> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with
> diagnostics:
> object 'table_pre' not found
>
> However, I did confirm my package with R CMD BUILD and CHECK before
> committing, and there was no errors and warnings.
>
> I really don't know what is the problem.
>
> Does anyone have the same error before?
>
> Many Thanks,
>
> Ti-Tai Wang
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=
>
>

 --
 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

>>>
>>
>> --
>> 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
>>
>
> --
> 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
___
Bioc-devel@r-project.org mailing list

Re: [Bioc-devel] xps build problem on veracruz2

[Hervé Pagès]

On 04/20/2017 03:01 PM, cstrato wrote:

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_90056_-2390247=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=GfzgU1Ibm_scFWO58Mv_ZfxKtn-FSJgkxMW1ZBYK1Vs=

This means, that users of xps seem to be willing to disable csrutil.


I'm not a statistician but I wouldn't draw conclusions from a sample
of size 1. Mac users who cannot install xps on their machine will
use something else, or, if they desperately need xps, they will
grab a Linux box.

Sorry but disabling SIP on our Mac builders is not an option.





However, I just realized that there may be an even greater problem,
namely, which version of ROOT should a user install?

People can download ROOT binaries built with XCode 7.x from:
https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_content_release-2D53436=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q0hKDI_veZEYmjrYbsK1Xqu--fGdfl_JmfSKLygl_dg=LByiYPyOfsHnRc9oOqXOs9xMcfltktXgkTQ3sh5hKFc=
for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT from source?


As I said earlier, I compiled ROOT 5 from source on veracruz2.



With the help of my README file people could compile ROOT from source
for XCode 8.x.


However, you have mentioned that the CRAN people are using clang 4.0.0
for producing the Mac binaries of R and CRAN packages and thus you are
using the same on veracruz2.


Yes.



Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which
is not officially supported by Apple?


With clang 4.0.0.



The question is whether xps built with this version of ROOT will work
with the ROOT binaries which people can download from ROOT?


I guess someone will need to figure this out.

Note that if people need to compile their own ROOT anyway in order to
be able to use the xps binary we distribute, then they should also be
able to install xps from source. So that defeats the purpose of
providing a binary in the first place.

Cheers,
H.



Best regards,
Christian



On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc

H.


won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.


On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear
that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people
(when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:


1, Is there any reason that you do not want to 'csrutil disable'?


2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since you say that the problem can be solved by adding the -rpath flag
when linking, I assume that I have to change  the following line in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint how to
change
it?


3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=




Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?


4, Googling for the DYLD_LIBRARY_PATH problem I have also found the
following discussion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk=




There, one answer mentioned:
'Also, rpath is a good idea. Also 

Re: [Bioc-devel] Object not found in vignette

[Michael Lawrence]

Did you "svn add" the file?

On Thu, Apr 20, 2017 at 3:10 PM, 王棣台  wrote:
> I find that my data file will not change after I did any commit.
> That might be the problem.
> Is there anything I forget to do?
>
> Ti-Tai
> 
> 從: Hervé Pagès [hpa...@fredhutch.org]
> 寄件日期: 2017年4月21日 上午 06:00
> 至: 王棣台; bioc-devel@r-project.org
> 主旨: Re: [Bioc-devel] Object not found in vignette
>
> Also recently you bumped the version from 1.1.* to 1.2.*
> then went back to 1.1.* again. As a result the version that
> is available via biocLite() is 1.2.2, as reflected on the package
> landing page:
>
>https://bioconductor.org/packages/3.5/bioc/html/anamiR.html
>
> Any change you do to your package now won't propagate unless
> you bump the version to > 1.2.2.
>
> H.
>
> On 04/20/2017 02:52 PM, 王棣台 wrote:
>> it should be in my package since anamiR version 1.1.8
>> That is weird.
>>
>> Ti-Tai
>> 
>> 從: Hervé Pagès [hpa...@fredhutch.org]
>> 寄件日期: 2017年4月21日 上午 05:49
>> 至: 王棣台; bioc-devel@r-project.org
>> 主旨: Re: [Bioc-devel] Object not found in vignette
>>
>> On 04/20/2017 02:45 PM, Hervé Pagès wrote:
>>> On 04/20/2017 02:36 PM, 王棣台 wrote:
 That missing object is a list format data generated by myself,
 so I don't think it would be about Depends, Imports, or Suggests.
 Except this one, other generated data can be found.
>>>
>>> And where did you put this data set so that data(table_pre) can
>>> find it?
>>
>> I mean the other generated data sets can be found because they are
>> in your package but I don't see the table_pre data set there. Did you forget
>> to commit it?
>>
>> H.
>>
>>>
>>> H.
>>>

 Ti-Tai

 
 從: Hervé Pagès [hpa...@fredhutch.org]
 寄件日期: 2017年4月21日 上午 05:16
 至: 王棣台; bioc-devel@r-project.org
 主旨: Re: [Bioc-devel] Object not found in vignette

 Why don't you give us the name of your package so we can look
 at it? I suspect something is missing in your Depends, Imports,
 or Suggests field. Works for you because you have the missing
 package installed on your machine but not on the build machine
 because the package is missing there. The build system (and your
 users) doesn't have this package so the vignette fails there.
 By adding the package to Depends, Imports, or Suggests, you let
 the build system know that this package needs to be installed
 before it tries to build the vignette.

 H.

 On 04/20/2017 01:51 PM, 王棣台 wrote:
> Hi all,
>
> I kept getting the same Error from BUILD REPORT:
>
>
> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with
> diagnostics:
> object 'table_pre' not found
>
> However, I did confirm my package with R CMD BUILD and CHECK before
> committing, and there was no errors and warnings.
>
> I really don't know what is the problem.
>
> Does anyone have the same error before?
>
> Many Thanks,
>
> Ti-Tai Wang
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=
>
>

 --
 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

>>>
>>
>> --
>> 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
>>
>
> --
> 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

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

Re: [Bioc-devel] Object not found in vignette

[王棣台]

I find that my data file will not change after I did any commit.
That might be the problem.
Is there anything I forget to do?

Ti-Tai

��: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 06:00
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Also recently you bumped the version from 1.1.* to 1.2.*
then went back to 1.1.* again. As a result the version that
is available via biocLite() is 1.2.2, as reflected on the package
landing page:

   https://bioconductor.org/packages/3.5/bioc/html/anamiR.html

Any change you do to your package now won't propagate unless
you bump the version to > 1.2.2.

H.

On 04/20/2017 02:52 PM, 王棣台 wrote:
> it should be in my package since anamiR version 1.1.8
> That is weird.
>
> Ti-Tai
> 
> ��: Hervé Pagès [hpa...@fredhutch.org]
> 寄件日期: 2017年4月21日 上午 05:49
> 至: 王棣台; bioc-devel@r-project.org
> 主旨: Re: [Bioc-devel] Object not found in vignette
>
> On 04/20/2017 02:45 PM, Hervé Pagès wrote:
>> On 04/20/2017 02:36 PM, 王棣台 wrote:
>>> That missing object is a list format data generated by myself,
>>> so I don't think it would be about Depends, Imports, or Suggests.
>>> Except this one, other generated data can be found.
>>
>> And where did you put this data set so that data(table_pre) can
>> find it?
>
> I mean the other generated data sets can be found because they are
> in your package but I don't see the table_pre data set there. Did you forget
> to commit it?
>
> H.
>
>>
>> H.
>>
>>>
>>> Ti-Tai
>>>
>>> 
>>> ��: Hervé Pagès [hpa...@fredhutch.org]
>>> 寄件日期: 2017年4月21日 上午 05:16
>>> 至: 王棣台; bioc-devel@r-project.org
>>> 主旨: Re: [Bioc-devel] Object not found in vignette
>>>
>>> Why don't you give us the name of your package so we can look
>>> at it? I suspect something is missing in your Depends, Imports,
>>> or Suggests field. Works for you because you have the missing
>>> package installed on your machine but not on the build machine
>>> because the package is missing there. The build system (and your
>>> users) doesn't have this package so the vignette fails there.
>>> By adding the package to Depends, Imports, or Suggests, you let
>>> the build system know that this package needs to be installed
>>> before it tries to build the vignette.
>>>
>>> H.
>>>
>>> On 04/20/2017 01:51 PM, 王棣台 wrote:
 Hi all,

 I kept getting the same Error from BUILD REPORT:


 Error: processing vignette 'IntroductionToanamiR.Rmd' failed with
 diagnostics:
 object 'table_pre' not found

 However, I did confirm my package with R CMD BUILD and CHECK before
 committing, and there was no errors and warnings.

 I really don't know what is the problem.

 Does anyone have the same error before?

 Many Thanks,

 Ti-Tai Wang

   [[alternative HTML version deleted]]

 ___
 Bioc-devel@r-project.org mailing list
 https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=


>>>
>>> --
>>> 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
>>>
>>
>
> --
> 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
>

--
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] Object not found in vignette

[王棣台]

Okay,
I will try to commit it again.

Ti-Tai


��: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 06:00
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Also recently you bumped the version from 1.1.* to 1.2.*
then went back to 1.1.* again. As a result the version that
is available via biocLite() is 1.2.2, as reflected on the package
landing page:

   https://bioconductor.org/packages/3.5/bioc/html/anamiR.html

Any change you do to your package now won't propagate unless
you bump the version to > 1.2.2.

H.

On 04/20/2017 02:52 PM, 王棣台 wrote:
> it should be in my package since anamiR version 1.1.8
> That is weird.
>
> Ti-Tai
> 
> ��: Hervé Pagès [hpa...@fredhutch.org]
> 寄件日期: 2017年4月21日 上午 05:49
> 至: 王棣台; bioc-devel@r-project.org
> 主旨: Re: [Bioc-devel] Object not found in vignette
>
> On 04/20/2017 02:45 PM, Hervé Pagès wrote:
>> On 04/20/2017 02:36 PM, 王棣台 wrote:
>>> That missing object is a list format data generated by myself,
>>> so I don't think it would be about Depends, Imports, or Suggests.
>>> Except this one, other generated data can be found.
>>
>> And where did you put this data set so that data(table_pre) can
>> find it?
>
> I mean the other generated data sets can be found because they are
> in your package but I don't see the table_pre data set there. Did you forget
> to commit it?
>
> H.
>
>>
>> H.
>>
>>>
>>> Ti-Tai
>>>
>>> 
>>> ��: Hervé Pagès [hpa...@fredhutch.org]
>>> 寄件日期: 2017年4月21日 上午 05:16
>>> 至: 王棣台; bioc-devel@r-project.org
>>> 主旨: Re: [Bioc-devel] Object not found in vignette
>>>
>>> Why don't you give us the name of your package so we can look
>>> at it? I suspect something is missing in your Depends, Imports,
>>> or Suggests field. Works for you because you have the missing
>>> package installed on your machine but not on the build machine
>>> because the package is missing there. The build system (and your
>>> users) doesn't have this package so the vignette fails there.
>>> By adding the package to Depends, Imports, or Suggests, you let
>>> the build system know that this package needs to be installed
>>> before it tries to build the vignette.
>>>
>>> H.
>>>
>>> On 04/20/2017 01:51 PM, 王棣台 wrote:
 Hi all,

 I kept getting the same Error from BUILD REPORT:


 Error: processing vignette 'IntroductionToanamiR.Rmd' failed with
 diagnostics:
 object 'table_pre' not found

 However, I did confirm my package with R CMD BUILD and CHECK before
 committing, and there was no errors and warnings.

 I really don't know what is the problem.

 Does anyone have the same error before?

 Many Thanks,

 Ti-Tai Wang

   [[alternative HTML version deleted]]

 ___
 Bioc-devel@r-project.org mailing list
 https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=


>>>
>>> --
>>> 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
>>>
>>
>
> --
> 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
>

--
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] xps build problem on veracruz2

[cstrato]

Dear Herve,

Doing 'csrutil disable' does indeed solve the problem, since:

1, in this way I was able to build xps on Mac OS Sierra

2, in this way I could already help one user of xps, see:
https://support.bioconductor.org/p/90056/#90247

This means, that users of xps seem to be willing to disable csrutil.



However, I just realized that there may be an even greater problem, 
namely, which version of ROOT should a user install?


People can download ROOT binaries built with XCode 7.x from:
https://root.cern.ch/content/release-53436
for OS X 10.10 and 10.11.

Thus for El Capitan they can download the following binaries:
- root_v5.34.36.macosx64-10.11-clang70.dmg
- root_v5.34.36.macosx64-10.11-clang70.tar.gz

Did you install one of those binaries or did you compile ROOT from source?

With the help of my README file people could compile ROOT from source 
for XCode 8.x.



However, you have mentioned that the CRAN people are using clang 4.0.0 
for producing the Mac binaries of R and CRAN packages and thus you are

using the same on veracruz2.

Did you compile ROOT with XCode 7 or 8 or did you use clang 4.0.0, which 
is not officially supported by Apple?


The question is whether xps built with this version of ROOT will work 
with the ROOT binaries which people can download from ROOT?


Best regards,
Christian



On 04/20/17 20:00, Hervé Pagès wrote:

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc

H.


won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.


On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:


1, Is there any reason that you do not want to 'csrutil disable'?


2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since you say that the problem can be solved by adding the -rpath flag
when linking, I assume that I have to change  the following line in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint how to change
it?


3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=



Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?


4, Googling for the DYLD_LIBRARY_PATH problem I have also found the
following discussion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk=



There, one answer mentioned:
'Also, rpath is a good idea. Also see install_name_tool, which can
change the load paths of libraries.'

Doing a search for 'install_name_tool' I found:
https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_2985315_using-2Dinstall-2Dname-2Dtool-2Dwhats-2Dgoing-2Dwrong=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=r5LiHlxkGAeJAcciwteD2XD6ffNtWLiknvcIj9EJL8E=



There, one answer mentioned (see also $man install_name_tool):
'Having experimented more: install_name_tool -id newname file will do
the trick.'

See also:
https://urldefense.proofpoint.com/v2/url?u=http-3A__qin.laya.com_tech-5Fcoding-5Fhelp_dylib-5Flinking.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo=




Do you think that either using the environment variable LD_RUN_PATH or
using 'install_name_tool' could solve the problem without having to use
'-rpath'?


Thank you in advance.
Best regards,
Christian



On 04/19/17 22:51, Hervé Pagès wrote:

Hi Christian,

So I installed ROOT 5 

Re: [Bioc-devel] Object not found in vignette

[Hervé Pagès]

Also recently you bumped the version from 1.1.* to 1.2.*
then went back to 1.1.* again. As a result the version that
is available via biocLite() is 1.2.2, as reflected on the package
landing page:

  https://bioconductor.org/packages/3.5/bioc/html/anamiR.html

Any change you do to your package now won't propagate unless
you bump the version to > 1.2.2.

H.

On 04/20/2017 02:52 PM, 王棣台 wrote:

it should be in my package since anamiR version 1.1.8
That is weird.

Ti-Tai

從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:49
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:45 PM, Hervé Pagès wrote:

On 04/20/2017 02:36 PM, 王棣台 wrote:

That missing object is a list format data generated by myself,
so I don't think it would be about Depends, Imports, or Suggests.
Except this one, other generated data can be found.


And where did you put this data set so that data(table_pre) can
find it?


I mean the other generated data sets can be found because they are
in your package but I don't see the table_pre data set there. Did you forget
to commit it?

H.



H.



Ti-Tai


從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:16
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Why don't you give us the name of your package so we can look
at it? I suspect something is missing in your Depends, Imports,
or Suggests field. Works for you because you have the missing
package installed on your machine but not on the build machine
because the package is missing there. The build system (and your
users) doesn't have this package so the vignette fails there.
By adding the package to Depends, Imports, or Suggests, you let
the build system know that this package needs to be installed
before it tries to build the vignette.

H.

On 04/20/2017 01:51 PM, 王棣台 wrote:

Hi all,

I kept getting the same Error from BUILD REPORT:


Error: processing vignette 'IntroductionToanamiR.Rmd' failed with
diagnostics:
object 'table_pre' not found

However, I did confirm my package with R CMD BUILD and CHECK before
committing, and there was no errors and warnings.

I really don't know what is the problem.

Does anyone have the same error before?

Many Thanks,

Ti-Tai Wang

  [[alternative HTML version deleted]]

___
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--
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





--
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



--
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] Object not found in vignette

[王棣台]

No,
I definitely have committed it since version 1.1.8
and I can see it right now in my anamiR/data files.

Ti-Tai

��: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:53
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:50 PM, 王棣台 wrote:
> I put in the anamiR/data/
> Just like other data I used in the vignette.

As I said, I don't see it there. According to data(package="anamiR"), the
data sets available in your package are:

Data sets in package ‘anamiR’:

egSymb  A table with information of gene symbol and
 gene ID
kegg.gs KEGG pathways with gene set information
mirna   miRNA expression data about breast cancer
mrnamRNA expression data about breast cancer
pheno.mirna phenotype data of 'mirna' about breast cancer
pheno.mrna  phenotype data of 'mrna' about breast cancer

So again, did you forget to commit it to svn, or did you add it to the
wrong place?

H.

>
> Ti-Tai
> 
> ��: Hervé Pagès [hpa...@fredhutch.org]
> 寄件日期: 2017年4月21日 上午 05:45
> 至: 王棣台; bioc-devel@r-project.org
> 主旨: Re: [Bioc-devel] Object not found in vignette
>
> On 04/20/2017 02:36 PM, 王棣台 wrote:
>> That missing object is a list format data generated by myself,
>> so I don't think it would be about Depends, Imports, or Suggests.
>> Except this one, other generated data can be found.
>
> And where did you put this data set so that data(table_pre) can
> find it?
>
> H.
>
>>
>> Ti-Tai
>>
>> 
>> ��: Hervé Pagès [hpa...@fredhutch.org]
>> 寄件日期: 2017年4月21日 上午 05:16
>> 至: 王棣台; bioc-devel@r-project.org
>> 主旨: Re: [Bioc-devel] Object not found in vignette
>>
>> Why don't you give us the name of your package so we can look
>> at it? I suspect something is missing in your Depends, Imports,
>> or Suggests field. Works for you because you have the missing
>> package installed on your machine but not on the build machine
>> because the package is missing there. The build system (and your
>> users) doesn't have this package so the vignette fails there.
>> By adding the package to Depends, Imports, or Suggests, you let
>> the build system know that this package needs to be installed
>> before it tries to build the vignette.
>>
>> H.
>>
>> On 04/20/2017 01:51 PM, 王棣台 wrote:
>>> Hi all,
>>>
>>> I kept getting the same Error from BUILD REPORT:
>>>
>>>
>>> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with 
>>> diagnostics:
>>> object 'table_pre' not found
>>>
>>> However, I did confirm my package with R CMD BUILD and CHECK before 
>>> committing, and there was no errors and warnings.
>>>
>>> I really don't know what is the problem.
>>>
>>> Does anyone have the same error before?
>>>
>>> Many Thanks,
>>>
>>> Ti-Tai Wang
>>>
>>>   [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=
>>>
>>
>> --
>> 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
>>
>
> --
> 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
>

--
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
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Re: [Bioc-devel] Object not found in vignette

[Hervé Pagès]

On 04/20/2017 02:50 PM, 王棣台 wrote:

I put in the anamiR/data/
Just like other data I used in the vignette.


As I said, I don't see it there. According to data(package="anamiR"), the
data sets available in your package are:

Data sets in package ‘anamiR’:

egSymb  A table with information of gene symbol and
gene ID
kegg.gs KEGG pathways with gene set information
mirna   miRNA expression data about breast cancer
mrnamRNA expression data about breast cancer
pheno.mirna phenotype data of 'mirna' about breast cancer
pheno.mrna  phenotype data of 'mrna' about breast cancer

So again, did you forget to commit it to svn, or did you add it to the
wrong place?

H.



Ti-Tai

從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:45
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:36 PM, 王棣台 wrote:

That missing object is a list format data generated by myself,
so I don't think it would be about Depends, Imports, or Suggests.
Except this one, other generated data can be found.


And where did you put this data set so that data(table_pre) can
find it?

H.



Ti-Tai


從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:16
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Why don't you give us the name of your package so we can look
at it? I suspect something is missing in your Depends, Imports,
or Suggests field. Works for you because you have the missing
package installed on your machine but not on the build machine
because the package is missing there. The build system (and your
users) doesn't have this package so the vignette fails there.
By adding the package to Depends, Imports, or Suggests, you let
the build system know that this package needs to be installed
before it tries to build the vignette.

H.

On 04/20/2017 01:51 PM, 王棣台 wrote:

Hi all,

I kept getting the same Error from BUILD REPORT:


Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics:
object 'table_pre' not found

However, I did confirm my package with R CMD BUILD and CHECK before committing, 
and there was no errors and warnings.

I really don't know what is the problem.

Does anyone have the same error before?

Many Thanks,

Ti-Tai Wang

  [[alternative HTML version deleted]]

___
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https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=



--
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



--
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



--
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] Object not found in vignette

[王棣台]

it should be in my package since anamiR version 1.1.8
That is weird.

Ti-Tai

��: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:49
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:45 PM, Hervé Pagès wrote:
> On 04/20/2017 02:36 PM, 王棣台 wrote:
>> That missing object is a list format data generated by myself,
>> so I don't think it would be about Depends, Imports, or Suggests.
>> Except this one, other generated data can be found.
>
> And where did you put this data set so that data(table_pre) can
> find it?

I mean the other generated data sets can be found because they are
in your package but I don't see the table_pre data set there. Did you forget
to commit it?

H.

>
> H.
>
>>
>> Ti-Tai
>>
>> 
>> ��: Hervé Pagès [hpa...@fredhutch.org]
>> 寄件日期: 2017年4月21日 上午 05:16
>> 至: 王棣台; bioc-devel@r-project.org
>> 主旨: Re: [Bioc-devel] Object not found in vignette
>>
>> Why don't you give us the name of your package so we can look
>> at it? I suspect something is missing in your Depends, Imports,
>> or Suggests field. Works for you because you have the missing
>> package installed on your machine but not on the build machine
>> because the package is missing there. The build system (and your
>> users) doesn't have this package so the vignette fails there.
>> By adding the package to Depends, Imports, or Suggests, you let
>> the build system know that this package needs to be installed
>> before it tries to build the vignette.
>>
>> H.
>>
>> On 04/20/2017 01:51 PM, 王棣台 wrote:
>>> Hi all,
>>>
>>> I kept getting the same Error from BUILD REPORT:
>>>
>>>
>>> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with
>>> diagnostics:
>>> object 'table_pre' not found
>>>
>>> However, I did confirm my package with R CMD BUILD and CHECK before
>>> committing, and there was no errors and warnings.
>>>
>>> I really don't know what is the problem.
>>>
>>> Does anyone have the same error before?
>>>
>>> Many Thanks,
>>>
>>> Ti-Tai Wang
>>>
>>>   [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=
>>>
>>>
>>
>> --
>> 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
>>
>

--
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
___
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Re: [Bioc-devel] Object not found in vignette

[王棣台]

I put in the anamiR/data/
Just like other data I used in the vignette.

Ti-Tai

��: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:45
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

On 04/20/2017 02:36 PM, 王棣台 wrote:
> That missing object is a list format data generated by myself,
> so I don't think it would be about Depends, Imports, or Suggests.
> Except this one, other generated data can be found.

And where did you put this data set so that data(table_pre) can
find it?

H.

>
> Ti-Tai
>
> 
> ��: Hervé Pagès [hpa...@fredhutch.org]
> 寄件日期: 2017年4月21日 上午 05:16
> 至: 王棣台; bioc-devel@r-project.org
> 主旨: Re: [Bioc-devel] Object not found in vignette
>
> Why don't you give us the name of your package so we can look
> at it? I suspect something is missing in your Depends, Imports,
> or Suggests field. Works for you because you have the missing
> package installed on your machine but not on the build machine
> because the package is missing there. The build system (and your
> users) doesn't have this package so the vignette fails there.
> By adding the package to Depends, Imports, or Suggests, you let
> the build system know that this package needs to be installed
> before it tries to build the vignette.
>
> H.
>
> On 04/20/2017 01:51 PM, 王棣台 wrote:
>> Hi all,
>>
>> I kept getting the same Error from BUILD REPORT:
>>
>>
>> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with 
>> diagnostics:
>> object 'table_pre' not found
>>
>> However, I did confirm my package with R CMD BUILD and CHECK before 
>> committing, and there was no errors and warnings.
>>
>> I really don't know what is the problem.
>>
>> Does anyone have the same error before?
>>
>> Many Thanks,
>>
>> Ti-Tai Wang
>>
>>   [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=
>>
>
> --
> 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
>

--
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
___
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Re: [Bioc-devel] Object not found in vignette

[Hervé Pagès]

On 04/20/2017 02:45 PM, Hervé Pagès wrote:

On 04/20/2017 02:36 PM, 王棣台 wrote:

That missing object is a list format data generated by myself,
so I don't think it would be about Depends, Imports, or Suggests.
Except this one, other generated data can be found.


And where did you put this data set so that data(table_pre) can
find it?


I mean the other generated data sets can be found because they are
in your package but I don't see the table_pre data set there. Did you forget
to commit it?

H.



H.



Ti-Tai


從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:16
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Why don't you give us the name of your package so we can look
at it? I suspect something is missing in your Depends, Imports,
or Suggests field. Works for you because you have the missing
package installed on your machine but not on the build machine
because the package is missing there. The build system (and your
users) doesn't have this package so the vignette fails there.
By adding the package to Depends, Imports, or Suggests, you let
the build system know that this package needs to be installed
before it tries to build the vignette.

H.

On 04/20/2017 01:51 PM, 王棣台 wrote:

Hi all,

I kept getting the same Error from BUILD REPORT:


Error: processing vignette 'IntroductionToanamiR.Rmd' failed with
diagnostics:
object 'table_pre' not found

However, I did confirm my package with R CMD BUILD and CHECK before
committing, and there was no errors and warnings.

I really don't know what is the problem.

Does anyone have the same error before?

Many Thanks,

Ti-Tai Wang

  [[alternative HTML version deleted]]

___
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--
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





--
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
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Re: [Bioc-devel] Object not found in vignette

[Hervé Pagès]

On 04/20/2017 02:36 PM, 王棣台 wrote:

That missing object is a list format data generated by myself,
so I don't think it would be about Depends, Imports, or Suggests.
Except this one, other generated data can be found.


And where did you put this data set so that data(table_pre) can
find it?

H.



Ti-Tai


從: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:16
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Why don't you give us the name of your package so we can look
at it? I suspect something is missing in your Depends, Imports,
or Suggests field. Works for you because you have the missing
package installed on your machine but not on the build machine
because the package is missing there. The build system (and your
users) doesn't have this package so the vignette fails there.
By adding the package to Depends, Imports, or Suggests, you let
the build system know that this package needs to be installed
before it tries to build the vignette.

H.

On 04/20/2017 01:51 PM, 王棣台 wrote:

Hi all,

I kept getting the same Error from BUILD REPORT:


Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics:
object 'table_pre' not found

However, I did confirm my package with R CMD BUILD and CHECK before committing, 
and there was no errors and warnings.

I really don't know what is the problem.

Does anyone have the same error before?

Many Thanks,

Ti-Tai Wang

  [[alternative HTML version deleted]]

___
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--
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



--
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

___
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Re: [Bioc-devel] Object not found in vignette

[王棣台]

That missing object is a list format data generated by myself,
so I don't think it would be about Depends, Imports, or Suggests.
Except this one, other generated data can be found.

Ti-Tai


��: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:16
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Why don't you give us the name of your package so we can look
at it? I suspect something is missing in your Depends, Imports,
or Suggests field. Works for you because you have the missing
package installed on your machine but not on the build machine
because the package is missing there. The build system (and your
users) doesn't have this package so the vignette fails there.
By adding the package to Depends, Imports, or Suggests, you let
the build system know that this package needs to be installed
before it tries to build the vignette.

H.

On 04/20/2017 01:51 PM, 王棣台 wrote:
> Hi all,
>
> I kept getting the same Error from BUILD REPORT:
>
>
> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics:
> object 'table_pre' not found
>
> However, I did confirm my package with R CMD BUILD and CHECK before 
> committing, and there was no errors and warnings.
>
> I really don't know what is the problem.
>
> Does anyone have the same error before?
>
> Many Thanks,
>
> Ti-Tai Wang
>
>   [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=TK-8woT9u1jslARFhHX9Y_pg-0Cg9S5vwIyvMX86pHU=3gO7lG40pXAtK-3RkKJ-yhJdwqUw-NZwBORf4PaN7xg=
>

--
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
___
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Re: [Bioc-devel] Object not found in vignette

[王棣台]

Hi,

The name of my package is anamiR.
it is an object which I try to use in vignette as an example data.

Ti-Tai Wang


��: Hervé Pagès [hpa...@fredhutch.org]
寄件日期: 2017年4月21日 上午 05:16
至: 王棣台; bioc-devel@r-project.org
主旨: Re: [Bioc-devel] Object not found in vignette

Why don't you give us the name of your package so we can look
at it? I suspect something is missing in your Depends, Imports,
or Suggests field. Works for you because you have the missing
package installed on your machine but not on the build machine
because the package is missing there. The build system (and your
users) doesn't have this package so the vignette fails there.
By adding the package to Depends, Imports, or Suggests, you let
the build system know that this package needs to be installed
before it tries to build the vignette.

H.

On 04/20/2017 01:51 PM, 王棣台 wrote:
> Hi all,
>
> I kept getting the same Error from BUILD REPORT:
>
>
> Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics:
> object 'table_pre' not found
>
> However, I did confirm my package with R CMD BUILD and CHECK before 
> committing, and there was no errors and warnings.
>
> I really don't know what is the problem.
>
> Does anyone have the same error before?
>
> Many Thanks,
>
> Ti-Tai Wang
>
>   [[alternative HTML version deleted]]
>
> ___
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>

--
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Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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E-mail: hpa...@fredhutch.org
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Re: [Bioc-devel] Object not found in vignette

[Hervé Pagès]

Why don't you give us the name of your package so we can look
at it? I suspect something is missing in your Depends, Imports,
or Suggests field. Works for you because you have the missing
package installed on your machine but not on the build machine
because the package is missing there. The build system (and your
users) doesn't have this package so the vignette fails there.
By adding the package to Depends, Imports, or Suggests, you let
the build system know that this package needs to be installed
before it tries to build the vignette.

H.

On 04/20/2017 01:51 PM, 王棣台 wrote:

Hi all,

I kept getting the same Error from BUILD REPORT:


Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics:
object 'table_pre' not found

However, I did confirm my package with R CMD BUILD and CHECK before committing, 
and there was no errors and warnings.

I really don't know what is the problem.

Does anyone have the same error before?

Many Thanks,

Ti-Tai Wang

[[alternative HTML version deleted]]

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--
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

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[Bioc-devel] Object not found in vignette

[王棣台]

Hi all,

I kept getting the same Error from BUILD REPORT:


Error: processing vignette 'IntroductionToanamiR.Rmd' failed with diagnostics:
object 'table_pre' not found

However, I did confirm my package with R CMD BUILD and CHECK before committing, 
and there was no errors and warnings.

I really don't know what is the problem.

Does anyone have the same error before?

Many Thanks,

Ti-Tai Wang

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Issue with including vignettes without building package

[Zhian Kamvar]

Perhaps you could add a Makefile with a rule that compiles the vignettes into 
the inst/doc directory? This might avoid the build process.

-
Zhian N. Kamvar, Ph. D.
Postdoctoral Researcher (Everhart Lab)
Department of Plant Pathology
University of Nebraska-Lincoln



> On Apr 20, 2017, at 15:30 , Alexandre Courtiol  
> wrote:
> 
> Thanks but I don't think so, that would imply them to rebuild the
> vignettes, which is exactly what I want to avoid.
> Without knitr cached chunk it would take forever on their laptops and they
> would also need to install tons of packages...
> ++
> 
> On 20 April 2017 at 21:01, Sven E Templer  > wrote:
> 
>> Hi Alex,
>> 
>> 
>> what if you run
>> 
>> devtools::install_github(build_vignettes = TRUE)
>> 
>> on your students computer?
>> 
>> See ?devtools::install
>> 
>> 
>> Best,
>> 
>> Sven
>> 
>> 
>>> On 20. Apr 2017, at 15:09, Alexandre Courtiol <
>> alexandre.court...@gmail.com> wrote:
>>> 
>>> Dear all,
>>> 
>>> I am using a package for teaching:
>>> my slides are html vignettes, and it is convenient for students to
>> control
>>> which packages they must install, provide code and datasets.
>>> 
>>> As I am often editing the package live during the course, it would be
>> great
>>> if I could just push to github and that the student would just have to
>> run
>>> a devtools::install_github() to get my updated vignettes. I would rather
>>> not to have to build the package before pushing to save time.
>>> 
>>> The issues is that I do not want to build the vignettes on install as
>> they
>>> are very slow to build. On my computer however it is quick because I have
>>> cached the knitr chunks output. So I was hoping to just have to run
>>> devtools::build_vignettes() on my machine before pushing the files
>> thereby
>>> created (./inst/doc) and that the student could just
>>> devtools::install_github().
>>> 
>>> I cannot make this work: no vignettes are found after install. When I do
>>> check the repository beeing installed on their computers, the html, Rmd
>> and
>>> R files corresponding to the vignettes are present in ./doc, so it is not
>>> an issue of having the wrong .gitgnore configuration.
>>> 
>>> I have read about many vignettes related issues on the net, but I did not
>>> find something dealing with this precise issue.
>>> 
>>> PS: I know about the R.rsp hack, but I would prefer to find a solution
>> more
>>> direct.
>>> 
>>> Best,
>>> 
>>> Alex
>>> 
>>> 
>>> 
>>> 
>>> --
>>> Alexandre Courtiol
>>> 
>>> http://sites.google.com/site/alexandrecourtiol/home
>>> 
>>> *"Science is the belief in the ignorance of experts"*, R. Feynman
>>> 
>>>  [[alternative HTML version deleted]]
>>> 
>>> __
>>> R-package-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> 
>> 
> 
> 
> -- 
> Alexandre Courtiol
> 
> http://sites.google.com/site/alexandrecourtiol/home 
> 
> 
> *"Science is the belief in the ignorance of experts"*, R. Feynman
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-package-devel@r-project.org  mailing 
> list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel 
> 

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Re: [R-pkg-devel] Issue with including vignettes without building package

[Alexandre Courtiol]

To rephrase my needs, I need to find a way to create the file
/Meta/vignette.rds at install, not build, as all other files for the
vignettes to run are being installed properly.
Has anyone managed to do that?
For now my horrible hack is to have a function calling the vignette through
a call to browseURL(paste0(find.package("XXX"), "/doc/")).
It opens the folder with all the vignette, but it is not as nice as opening
the index in the web browser.
Doing a browseURL on the index.html works but then the links do not... so
that does not help.
Best
Alex

On 20 April 2017 at 22:30, Alexandre Courtiol 
wrote:

> Thanks but I don't think so, that would imply them to rebuild the
> vignettes, which is exactly what I want to avoid.
> Without knitr cached chunk it would take forever on their laptops and they
> would also need to install tons of packages...
> ++
>
> On 20 April 2017 at 21:01, Sven E Templer  wrote:
>
>> Hi Alex,
>>
>>
>> what if you run
>>
>> devtools::install_github(build_vignettes = TRUE)
>>
>> on your students computer?
>>
>> See ?devtools::install
>>
>>
>> Best,
>>
>> Sven
>>
>>
>> > On 20. Apr 2017, at 15:09, Alexandre Courtiol <
>> alexandre.court...@gmail.com> wrote:
>> >
>> > Dear all,
>> >
>> > I am using a package for teaching:
>> > my slides are html vignettes, and it is convenient for students to
>> control
>> > which packages they must install, provide code and datasets.
>> >
>> > As I am often editing the package live during the course, it would be
>> great
>> > if I could just push to github and that the student would just have to
>> run
>> > a devtools::install_github() to get my updated vignettes. I would rather
>> > not to have to build the package before pushing to save time.
>> >
>> > The issues is that I do not want to build the vignettes on install as
>> they
>> > are very slow to build. On my computer however it is quick because I
>> have
>> > cached the knitr chunks output. So I was hoping to just have to run
>> > devtools::build_vignettes() on my machine before pushing the files
>> thereby
>> > created (./inst/doc) and that the student could just
>> > devtools::install_github().
>> >
>> > I cannot make this work: no vignettes are found after install. When I do
>> > check the repository beeing installed on their computers, the html, Rmd
>> and
>> > R files corresponding to the vignettes are present in ./doc, so it is
>> not
>> > an issue of having the wrong .gitgnore configuration.
>> >
>> > I have read about many vignettes related issues on the net, but I did
>> not
>> > find something dealing with this precise issue.
>> >
>> > PS: I know about the R.rsp hack, but I would prefer to find a solution
>> more
>> > direct.
>> >
>> > Best,
>> >
>> > Alex
>> >
>> >
>> >
>> >
>> > --
>> > Alexandre Courtiol
>> >
>> > http://sites.google.com/site/alexandrecourtiol/home
>> >
>> > *"Science is the belief in the ignorance of experts"*, R. Feynman
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > __
>> > R-package-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>>
>
>
> --
> Alexandre Courtiol
>
> http://sites.google.com/site/alexandrecourtiol/home
>
> *"Science is the belief in the ignorance of experts"*, R. Feynman
>



-- 
Alexandre Courtiol

http://sites.google.com/site/alexandrecourtiol/home

*"Science is the belief in the ignorance of experts"*, R. Feynman

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Re: [R-pkg-devel] Issue with including vignettes without building package

[Alexandre Courtiol]

Thanks but I don't think so, that would imply them to rebuild the
vignettes, which is exactly what I want to avoid.
Without knitr cached chunk it would take forever on their laptops and they
would also need to install tons of packages...
++

On 20 April 2017 at 21:01, Sven E Templer  wrote:

> Hi Alex,
>
>
> what if you run
>
> devtools::install_github(build_vignettes = TRUE)
>
> on your students computer?
>
> See ?devtools::install
>
>
> Best,
>
> Sven
>
>
> > On 20. Apr 2017, at 15:09, Alexandre Courtiol <
> alexandre.court...@gmail.com> wrote:
> >
> > Dear all,
> >
> > I am using a package for teaching:
> > my slides are html vignettes, and it is convenient for students to
> control
> > which packages they must install, provide code and datasets.
> >
> > As I am often editing the package live during the course, it would be
> great
> > if I could just push to github and that the student would just have to
> run
> > a devtools::install_github() to get my updated vignettes. I would rather
> > not to have to build the package before pushing to save time.
> >
> > The issues is that I do not want to build the vignettes on install as
> they
> > are very slow to build. On my computer however it is quick because I have
> > cached the knitr chunks output. So I was hoping to just have to run
> > devtools::build_vignettes() on my machine before pushing the files
> thereby
> > created (./inst/doc) and that the student could just
> > devtools::install_github().
> >
> > I cannot make this work: no vignettes are found after install. When I do
> > check the repository beeing installed on their computers, the html, Rmd
> and
> > R files corresponding to the vignettes are present in ./doc, so it is not
> > an issue of having the wrong .gitgnore configuration.
> >
> > I have read about many vignettes related issues on the net, but I did not
> > find something dealing with this precise issue.
> >
> > PS: I know about the R.rsp hack, but I would prefer to find a solution
> more
> > direct.
> >
> > Best,
> >
> > Alex
> >
> >
> >
> >
> > --
> > Alexandre Courtiol
> >
> > http://sites.google.com/site/alexandrecourtiol/home
> >
> > *"Science is the belief in the ignorance of experts"*, R. Feynman
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>


-- 
Alexandre Courtiol

http://sites.google.com/site/alexandrecourtiol/home

*"Science is the belief in the ignorance of experts"*, R. Feynman

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Re: [Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

[Michael Lawrence]

Thanks for pointing out these issues. I have a fix that I will commit soon.

Btw, I would never have seen the post on Stack Overflow. It's best to
report bugs on the bugzilla.

Michael

On Thu, Apr 20, 2017 at 8:30 AM, Andrzej Oleś  wrote:
> Hi all,
>
> I recently encountered some unexpected behavior with S4 generics
> dispatching on `...`, which I described in
> http://stackoverflow.com/questions/43499203/use-callnextmethod-with-dotsmethods
>
> TL;DR: `callNextMethod()` doesn't work in methods dispatching on `...`, and
> arguments of such methods are resolved differently than the arguments of
> methods dispatching on formal arguments.
>
> Could this indicate a potential problem with the implementation of the
> `...` dispatch?
>
> Cheers,
> Andrzej
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Vignette update after change in git mirror repo

[Sean Davis]

Hi, Maia.

The git mirror is not used for building packages.  Instead, you will need
to commit to svn for changes to show up on Bioconductor.  See here for
details of working with git and svn together.

https://www.bioconductor.org/developers/how-to/git-mirrors/

If I misunderstood what you are saying, could you clarify a bit?

Sean


On Thu, Apr 20, 2017 at 3:35 PM Maia Smith  wrote:

> How long does it take for the html vignette to update after a change in the
> git mirror has taken place? I changed my code in the git mirror a few days
> ago, and the html vignette hasn't incorporated these changes yet.
>
> Thanks in advance for your help.
>
> Maia
>
> [[alternative HTML version deleted]]
>
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[Bioc-devel] Vignette update after change in git mirror repo

[Maia Smith]

How long does it take for the html vignette to update after a change in the
git mirror has taken place? I changed my code in the git mirror a few days
ago, and the html vignette hasn't incorporated these changes yet.

Thanks in advance for your help.

Maia

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Re: [R-pkg-devel] Issue with including vignettes without building package

[Sven E Templer]

Hi Alex,


what if you run

devtools::install_github(build_vignettes = TRUE)

on your students computer?

See ?devtools::install


Best,

Sven


> On 20. Apr 2017, at 15:09, Alexandre Courtiol  
> wrote:
> 
> Dear all,
> 
> I am using a package for teaching:
> my slides are html vignettes, and it is convenient for students to control
> which packages they must install, provide code and datasets.
> 
> As I am often editing the package live during the course, it would be great
> if I could just push to github and that the student would just have to run
> a devtools::install_github() to get my updated vignettes. I would rather
> not to have to build the package before pushing to save time.
> 
> The issues is that I do not want to build the vignettes on install as they
> are very slow to build. On my computer however it is quick because I have
> cached the knitr chunks output. So I was hoping to just have to run
> devtools::build_vignettes() on my machine before pushing the files thereby
> created (./inst/doc) and that the student could just
> devtools::install_github().
> 
> I cannot make this work: no vignettes are found after install. When I do
> check the repository beeing installed on their computers, the html, Rmd and
> R files corresponding to the vignettes are present in ./doc, so it is not
> an issue of having the wrong .gitgnore configuration.
> 
> I have read about many vignettes related issues on the net, but I did not
> find something dealing with this precise issue.
> 
> PS: I know about the R.rsp hack, but I would prefer to find a solution more
> direct.
> 
> Best,
> 
> Alex
> 
> 
> 
> 
> -- 
> Alexandre Courtiol
> 
> http://sites.google.com/site/alexandrecourtiol/home
> 
> *"Science is the belief in the ignorance of experts"*, R. Feynman
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-package-devel@r-project.org mailing list
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Re: [Bioc-devel] xps build problem on veracruz2

[Hervé Pagès]

On 04/20/2017 10:59 AM, Hervé Pagès wrote:

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that

  ^^
oops, no double negative intended here. I meant, doing 'csrutil disable'
might help... etc

H.


won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.


On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:


1, Is there any reason that you do not want to 'csrutil disable'?


2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since you say that the problem can be solved by adding the -rpath flag
when linking, I assume that I have to change  the following line in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint how to change
it?


3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=


Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?


4, Googling for the DYLD_LIBRARY_PATH problem I have also found the
following discussion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk=


There, one answer mentioned:
'Also, rpath is a good idea. Also see install_name_tool, which can
change the load paths of libraries.'

Doing a search for 'install_name_tool' I found:
https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_2985315_using-2Dinstall-2Dname-2Dtool-2Dwhats-2Dgoing-2Dwrong=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=r5LiHlxkGAeJAcciwteD2XD6ffNtWLiknvcIj9EJL8E=


There, one answer mentioned (see also $man install_name_tool):
'Having experimented more: install_name_tool -id newname file will do
the trick.'

See also:
https://urldefense.proofpoint.com/v2/url?u=http-3A__qin.laya.com_tech-5Fcoding-5Fhelp_dylib-5Flinking.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo=



Do you think that either using the environment variable LD_RUN_PATH or
using 'install_name_tool' could solve the problem without having to use
'-rpath'?


Thank you in advance.
Best regards,
Christian



On 04/19/17 22:51, Hervé Pagès wrote:

Hi Christian,

So I installed ROOT 5 from source on veracruz2. It's in
/usr/local/root.

However, Apple's SIP (System Integrity Protection, new and
enabled by default on El Capitan) is getting in the way when
trying to install xps. That's because xps configure and build
process relies on DYLD_LIBRARY_PATH. Problem is that this
environment variable (and any other variables that control
dynamic loading) is not inherited by child processes when SIP
is on:

veracruz2:~ biocbuild$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!';
else echo 'nope!'; fi
yep!

veracruz2:~ biocbuild$ sh
sh-3.2$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo
'nope!'; fi
nope!

That breaks xps configure script:

veracruz2:~ biocbuild$ export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH

veracruz2:~ biocbuild$ echo $LD_LIBRARY_PATH
/usr/local/mysql/lib:/usr/local/root/lib/root:/ImageMagick-7.0.5/lib:/usr/local/ensembl-vep/htslib




veracruz2:~ biocbuild$ R CMD INSTALL xps
* installing to library
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘xps’ ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking 

Re: [Bioc-devel] xps build problem on veracruz2

[Hervé Pagès]

Hi Christian,

Disabling 'csrutil disable' might help xps on veracruz2 but that
won't help your end users.

I'm no expert in developing a package on Mac but other people on
this list are. Also R-SIG-Mac might be a good place to seek help
for this.

Cheers,
H.


On 04/20/2017 10:53 AM, cstrato wrote:

Dear Herve,

Thank you for your efforts to try to install xps. I am glad to hear that
you could build ROOT 5 from source.

It's a pity that Apple does no longer allow the use of
DYLD_LIBRARY_PATH. This seems to break the code of a lot of people (when
googling around).

I will try to change the build process and will see if I succeed.
However, at the moment I have a couple of questions:


1, Is there any reason that you do not want to 'csrutil disable'?


2, It is easy to delete the test for DYLD_LIBRARY_PATH in my
'configure.in' file, however, I have also to change the 'Makefile'.

Since you say that the problem can be solved by adding the -rpath flag
when linking, I assume that I have to change  the following line in my
'Makefile':
$(LD) -bundle $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) \
   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)

Since I am not familiar with -rpath can you give me a hint how to change
it?


3, There is a Wikipedia explanation for '-rpath', see:
https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Rpath=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=ge_d4eBoKDAggNWVQUzMVPAJy250VlZuPTXcPyr20HM=

Interestingly, there is the following line:

'Instead of specifying the -rpath to the linker, the environment
variable LD_RUN_PATH can be set to the same effect.'

Do you think that using LD_RUN_PATH would solve the problem?
If yes, then how?


4, Googling for the DYLD_LIBRARY_PATH problem I have also found the
following discussion:
https://urldefense.proofpoint.com/v2/url?u=https-3A__forums.macrumors.com_threads_is-2Dit-2Dok-2Dto-2Duse-2Ddyld-5Flibrary-5Fpath-2Don-2Dmac-2Dos-2Dx-2Dand-2Dwhat-25C2-2592s-2Dthe-2Ddynamic-2Dlibrary-2Dsearch.956258_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=yhLXARIG_RS1LNegc7tbjO1bayLOp7zy5-rzbtjCHIk=

There, one answer mentioned:
'Also, rpath is a good idea. Also see install_name_tool, which can
change the load paths of libraries.'

Doing a search for 'install_name_tool' I found:
https://urldefense.proofpoint.com/v2/url?u=http-3A__stackoverflow.com_questions_2985315_using-2Dinstall-2Dname-2Dtool-2Dwhats-2Dgoing-2Dwrong=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=r5LiHlxkGAeJAcciwteD2XD6ffNtWLiknvcIj9EJL8E=

There, one answer mentioned (see also $man install_name_tool):
'Having experimented more: install_name_tool -id newname file will do
the trick.'

See also:
https://urldefense.proofpoint.com/v2/url?u=http-3A__qin.laya.com_tech-5Fcoding-5Fhelp_dylib-5Flinking.html=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=kxgD4oa4CZeT4T7uLq2m3iVTvgvFB_RKN1Rf1KcxPk0=FL17xv1uuzR6UF59mgJstMQ-1seE1UeKDQVVXQgXnUo=


Do you think that either using the environment variable LD_RUN_PATH or
using 'install_name_tool' could solve the problem without having to use
'-rpath'?


Thank you in advance.
Best regards,
Christian



On 04/19/17 22:51, Hervé Pagès wrote:

Hi Christian,

So I installed ROOT 5 from source on veracruz2. It's in
/usr/local/root.

However, Apple's SIP (System Integrity Protection, new and
enabled by default on El Capitan) is getting in the way when
trying to install xps. That's because xps configure and build
process relies on DYLD_LIBRARY_PATH. Problem is that this
environment variable (and any other variables that control
dynamic loading) is not inherited by child processes when SIP
is on:

veracruz2:~ biocbuild$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!';
else echo 'nope!'; fi
yep!

veracruz2:~ biocbuild$ sh
sh-3.2$ if test "${DYLD_LIBRARY_PATH}"; then echo 'yep!'; else echo
'nope!'; fi
nope!

That breaks xps configure script:

veracruz2:~ biocbuild$ export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH

veracruz2:~ biocbuild$ echo $LD_LIBRARY_PATH
/usr/local/mysql/lib:/usr/local/root/lib/root:/ImageMagick-7.0.5/lib:/usr/local/ensembl-vep/htslib



veracruz2:~ biocbuild$ R CMD INSTALL xps
* installing to library
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘xps’ ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ANSI C... none needed
checking how to run the C preprocessor... clang -E
checking for gcc... (cached) clang

Re: [Rd] Intel MKL compiling issue

[Prof Brian Ripley]

There is nothing here indicating any kind of error, so no way to give 
any insights 


And please do follow the posting guide, including not posting HTML.

FWIW, I have tested R 3.4.0 RC (sic) with MKL 11.3, which is later than 
your 2013 ... (on x86_64 Fedora 24).



On 20/04/2017 10:39, jing hua zhao wrote:

Dear R-developers,


I would appreciate any insights over compiling R 3.4 with Intel MKL -- I have 
been successful until R 3.3.3 but now it stops complaining about pcre though it 
worked without Intel MKL as follows,


./configure LDFLAGS=-L/genetics/data/software/lib CFLAGS=-fPIC 
-I/genetics/data/software/include --enable-R-shlib


I have used,


export MKL_NUM_THREADS=15
export MKLROOT=/genetics/data/software/intel/composer_xe_2013.4.183/mkl
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MKLROOT/lib/intel64
/genetics/data/software/intel/composer_xe_2013.4.183/mkl/bin/mklvars.sh intel64
CPPFLAGS="-I/genetics/data/software/include -L/genetics/data/software/lib" \
./configure --prefix=/genetics/data/software --enable-R-shlib 
--enable-threads=posix --with-lapack \
 --with-blas="-fopenmp -m64 -I$MKLROOT/include -L$MKLROOT/lib/intel64 -lmkl_gf_lp64 
-lmkl_gnu_thread -lmkl_core -lpthread -lm"


Many thanks,



Jing Hua

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Emeritus Professor of Applied Statistics, University of Oxford

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[Rd] Problems with S4 methods dispatching on `...` (aka dotsMethods)

[Andrzej Oleś]

Hi all,

I recently encountered some unexpected behavior with S4 generics
dispatching on `...`, which I described in
http://stackoverflow.com/questions/43499203/use-callnextmethod-with-dotsmethods

TL;DR: `callNextMethod()` doesn't work in methods dispatching on `...`, and
arguments of such methods are resolved differently than the arguments of
methods dispatching on formal arguments.

Could this indicate a potential problem with the implementation of the
`...` dispatch?

Cheers,
Andrzej

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Re: [Rd] system/system2 and open file descriptors

[William Dunlap via R-devel]

In S+ on Unix-alikes we dealt with this issue by using fcntl(fd,
F_SETFD, 1) to set the close-on-exec flag on a file descriptor as soon
as we opened it.
Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Wed, Apr 19, 2017 at 8:40 PM, Winston Chang  wrote:
> In addition to the issue of a child process holding onto open files, the
> child process can also manipulate a file descriptor in a way that affects
> the parent process. For example, calling lseek() in the child process will
> move the file offset in the parent process.
>
> Here is a set of commands that demonstrates it. They can be copied and
> pasted in a terminal. What it does:
> - Creates C program that seeks to the beginning of a file descriptor, and
> compiles it to a program named "lseek".
> - Creates a file with some text in it.
> - Starts R. In R:
> - Opens the text file and reads the first line.
> - Runs lseek in a child process.
> - Reads the rest of the lines.
>
>
> echo "#include 
> int main(void) {
>   lseek(3, 0, SEEK_SET);
> }" > lseek.c
>
> gcc lseek.c -o lseek
>
> echo "line 1
> line 2
> line 3" > lines.txt
>
> R
> f <- file('lines.txt', 'r')
> cat(readLines(f, n = 1), sep = "\n")
> system('./lseek')
> cat(readLines(f), sep = "\n")
>
>
> Here's what it outputs:
>> f <- file('lines.txt', 'r')
>> cat(readLines(f, n = 1), sep = "\n")
> line 1
>> system('./lseek')
>> cat(readLines(f), sep = "\n")
> line 2
> line 3
> line 1
> line 2
> line 3
>
> The child process has changed what the parent process reads from the file.
> (I'm guessing that the reason readLines() prints out "line 2" and "line 3"
> before starting over is because it has already buffered the whole file
> before lseek is executed.)
>
> This is obviously a highly contrived case, but it illustrates what's
> possible. The other issue I mentioned, with child processes holding open
> files after the R process exits, is more likely to cause problems in the
> real world. That's actually how I encountered this issue in the first
> place: when restarting R inside of RStudio on a Mac, if there are any
> extant child processes started by system(), they keep some files open, and
> this causes RStudio to hang. (There's a fix in progress for RStudio for
> this particular issue.)
>
> -Winston
>
>
>
> On Tue, Apr 18, 2017 at 3:20 PM, Winston Chang 
> wrote:
>
>> It seems that the system() and system2() functions don't close file
>> descriptors between the fork() and exec() (on Unix platforms, of course).
>> This means that the child processes inherit open files and socket
>> connections.
>>
>> Running this (from a terminal) will result in the child process writing to
>> a file that was opened by R:
>>
>> R
>> f <- file('foo.txt', 'w')
>> system('echo "abc" >&3')
>>
>>
>>
>> You can also see the open files if you run the following:
>>   f <- file('foo.txt', 'w')
>>   system2('sleep', '100', wait=F)
>>
>> And then in another terminal:
>>   lsof -c R -c sleep
>> it will show that both the R and sleep processes have the file open:
>>   ...
>>   R   324 root3w   REG   0,480   4259 /foo.txt
>>   ...
>>   sleep   327 root3w   REG   0,480   4259 /foo.txt
>>
>>
>> This behavior can cause problems if R spawns a child process that outlives
>> the R process, but keeps open some resources.
>>
>> Would it be possible to add an option to close file descriptors for child
>> processes? It would be nice if that were the default, but I suspect that
>> making that change would break a lot of existing code.
>>
>> To take an example from the Python world, subprocess.Popen() has an
>> option, close_fds, which closes all file descriptors except 0, 1, and 2.
>>   https://docs.python.org/2/library/subprocess.html#popen-constructor
>>
>>
>> -Winston
>>
>
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>
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Re: [R-pkg-devel] R CMD check not finding my vignettes

[David Hugh-Jones]

Hi guys,

Thanks very much for all of your comments. I now have a good sense of what
the possibilities are, and I will think about what works best for my
package.

Cheers,
David


On 20 April 2017 at 14:42, Duncan Murdoch  wrote:

> On 20/04/2017 4:57 AM, Brian G. Peterson wrote:
>
>> David,
>>
>> I'd suggest creating a vignette for each of HTML and PDF, and including
>> a source file that contains the common code.  e.g. have a pdf header and
>> an html header file, and then include the 'main' Rmd as a child doc from
>> each header Rmd.  This way R CMD build could build both pdf and html
>> versions of the output.
>>
>
> That's another solution.  My suggestion would be simpler:  just pick one
> of PDF or HTML, and give the user instructions to produce the other if
> necessary, but don't produce it for them.
>
> Duncan Murdoch
>
>
>
>> Regards,
>>
>> Brian
>>
>> On 04/20/2017 03:38 AM, David Hugh-Jones wrote:
>>
>>> Hi Duncan,
>>>
>>> Thank you very much for taking the time to look at this.
>>>
>>> I tried rebuilding the tar file so as to include only the .Rmd files, not
>>> the HTML files, in 'vignettes':
>>>
>>> drwxr-xr-x  0 david  staff   0 20 Apr 09:21 huxtable/vignettes/
>>>
>>> -rw-r--r--  0 david  staff1633  6 Apr 16:26
>>> huxtable/vignettes/comparison.csv
>>>
>>> -rw-r--r--  0 david  staff6697  6 Apr 14:44
>>> huxtable/vignettes/design-principles.Rmd
>>>
>>> -rw-r--r--  0 david  staff5521  6 Apr 14:30
>>> huxtable/vignettes/huxreg.Rmd
>>>
>>> -rw-r--r--  0 david  staff   20552  6 Apr 16:19
>>> huxtable/vignettes/huxtable.Rmd
>>>
>>> -rw-r--r--  0 david  staff  22 17 Mar 00:19
>>> huxtable/vignettes/placeins-header.tex
>>>
>>>
>>> But when I run R CMD check, I still get the same warning:
>>>
>>> * checking package vignettes in ‘inst/doc’ ... WARNING
>>>
>>> Package vignettes without corresponding PDF/HTML:
>>>
>>>‘design-principles.Rmd’
>>>
>>>‘huxreg.Rmd’
>>>
>>>‘huxtable.Rmd’
>>>
>>> So, the warning does not seem to be related to the presence of HTML files
>>> in vignettes.
>>>
>>> I also tried manually removing .Rmd files from inst/doc (leaving them
>>> only
>>> in vignettes) but this still gave the same error.
>>>
>>> My goal here is that for package-specific reasons, I would like both pdf
>>> and HTML versions of my vignettes to be available (I am writing code that
>>> prints HTML and LaTeX tables and want my users to have examples of how
>>> both
>>> output formats work). This is why I build those files manually, and place
>>> them in inst/doc.
>>>
>>> Side comment: at the moment, I feel as if I am running through the
>>> combinatorics of including and excluding files from vignettes and
>>> inst/doc,
>>> without much insight into what I am doing. Would it be fair to say that
>>> the
>>> current system is not very easy to comprehend?
>>>
>>> Cheers,
>>>
>>> David
>>>
>>> On 19 April 2017 at 21:24, Duncan Murdoch 
>>> wrote:
>>>
>>> On 19/04/2017 1:00 PM, David Hugh-Jones wrote:

 Hi Uwe,
>
> I'm not sure if you ever got my off-list message with my tarball or
> subsequent messages. I can't send a tarball on-list - it gets rejected
> as
> too large - but here is a dropbox link. If you could confirm receipt,
> that
> would be extremely helpful!
>
> https://www.dropbox.com/s/179jrm19kx9o7dz/huxtable_0.2.0.tar.gz?dl=0
>
>
> Not sure if Uwe has had a chance to look, but I just ran R CMD check on
 your tarball using the latest version of R-devel.  It reported the
 following problems:

 * checking CRAN incoming feasibility ... NOTE
 Maintainer: ‘David Hugh-Jones ’

 Found the following (possibly) invalid URLs:
   URL: http://cran.rstudio.com/web/packages/huxtable/index.html
 From: README.md
 CRAN URL not in canonical form
   Canonical CRAN.R-project.org URLs use https.

 The URL for your package should be in the form

 https://CRAN.R-project.org/package=huxtable

 * checking top-level files ... NOTE
 Non-standard file/directory found at top level:
   ‘multirow.rds’

 I'm not sure where that file belongs, but not there.

 * checking files in ‘vignettes’ ... WARNING
 Files in the 'vignettes' directory newer than all files in 'inst/doc':
   ‘huxreg.html’, ‘huxtable.html’

 Those files shouldn't be in the vignettes directory, they are products
 of
 building the vignettes.  Only the source should normally be in the
 vignettes directory.

 * checking package vignettes in ‘inst/doc’ ... WARNING
 Package vignettes without corresponding PDF/HTML:
‘design-principles.Rmd’
‘huxreg.Rmd’
‘huxtable.Rmd’

 I think this is the warning you were asking about.  If I look at just
 the
 first of those files, I see that design-principles.Rmd exists in
 vignettes
 and is set 

Re: [Rd] ask.yes.no() function

[Duncan Murdoch]

On 20/04/2017 9:13 AM, Dirk Eddelbuettel wrote:


On 20 April 2017 at 09:33, Michael Sumner wrote:
| Perhaps worth pointing out "yesno" as a candidate:
|
| https://CRAN.R-project.org/package=yesno
| 

Not really as

 i)  base R will not have dependencies outside of it


Indeed, I'm looking for one that can be copied into base R.  The author 
can retain copyright, but we need to be able to offer it under our GPL 
license.




 ii) more importantly, Duncan asked for a good example of a "consistent" (as
 in: predictable) question function yet you submit one which by design
 *varies* answers to be less predictable.


Yes, there are reasons to have questions that vary randomly, but I think 
they don't apply to the situations where I want to use this.


Duncan Murdoch



Dirk

| Cheers, Mike
|
|
|
| On Wed, 19 Apr 2017 at 21:55 Duncan Murdoch 
| wrote:
|
| As described in
| , R base
| functions are currently inconsistent in asking interactive "yes/no" type
| questions. One solution to this is to have a function to do it, and to
| use it consistently.
|
|
|
|
| Rather than just writing such a function and possibly missing some
| desirable feature, I'd like to ask if anyone can point to an existing
| one that is perfect (or nearly perfect, and point out what changes would
| be desirable)?
|
| Duncan Murdoch
|
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
| --
| Dr. Michael Sumner
| Software and Database Engineer
| Australian Antarctic Division
| 203 Channel Highway
| Kingston Tasmania 7050 Australia
|
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|
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Re: [Rd] ask.yes.no() function

[Dirk Eddelbuettel]

On 20 April 2017 at 09:33, Michael Sumner wrote:
| Perhaps worth pointing out "yesno" as a candidate:
| 
| https://CRAN.R-project.org/package=yesno
| 

Not really as

 i)  base R will not have dependencies outside of it

 ii) more importantly, Duncan asked for a good example of a "consistent" (as
 in: predictable) question function yet you submit one which by design
 *varies* answers to be less predictable.

Dirk
 
| Cheers, Mike
| 
| 
| 
| On Wed, 19 Apr 2017 at 21:55 Duncan Murdoch 
| wrote:
| 
| As described in
| , R base
| functions are currently inconsistent in asking interactive "yes/no" type
| questions. One solution to this is to have a function to do it, and to
| use it consistently.
| 
| 
| 
| 
| Rather than just writing such a function and possibly missing some
| desirable feature, I'd like to ask if anyone can point to an existing
| one that is perfect (or nearly perfect, and point out what changes would
| be desirable)?
| 
| Duncan Murdoch
| 
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
| -- 
| Dr. Michael Sumner
| Software and Database Engineer
| Australian Antarctic Division
| 203 Channel Highway
| Kingston Tasmania 7050 Australia
| 
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| 
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-- 
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Re: [Rd] c() documentation after change; 'recursive' in "base" methods

[Martin Maechler]

> Suharto Anggono Suharto Anggono via R-devel 
> on Wed, 19 Apr 2017 22:50:41 + writes:

> In R 3.4.0 RC, argument list of 'c' as S4 generic function has become
> (x, ...) .
> However, "S4 methods" section in documentation of 'c' (c.Rd) is not 
updated yet.

Thank you, I've committed a change (72564 & 72565).

> Also, in R 3.4.0 RC, 'c' method of class "Date" ('c.Date') is still not 
explicitly documented.

yes, but that's true for other S3 methods, see below.

This is a bigger issue.  Thank you for raising it!  Look at

 R code --

(mc <- methods("c"))
## [1] c.bibentry*   c.Datec.difftimec.noquote 
c.numeric_version
## [6] c.person* c.POSIXct c.POSIXlt c.warnings
## and from `lcNSnm` below, you can see that these are from 'base',
## apart from {bibentry, person} which are from 'utils'
lc <- lapply(mc, function(nm) { f <- getAnywhere(nm) })
names(lc) <- sapply(lc, `[[`, "name")
str(lcwh <- lapply(lc, `[[`, "where"))
lcNSnm <- sub("^namespace:", '', sapply(lcwh, function(v) v[length(v)]))
lcNS <- lapply(lcNSnm, asNamespace)
str(lcMeths <-
sapply(names(lcNS), function(n) get(n, envir=lcNS[[n]], inherits=FALSE),
simplify = FALSE))
## $ c.bibentry   :function (..., recursive = FALSE)
## $ c.Date   :function (..., recursive = FALSE)
## $ c.difftime   :function (..., recursive = FALSE)
## $ c.noquote:function (..., recursive = FALSE)
## $ c.numeric_version:function (..., recursive = FALSE)
## $ c.person :function (..., recursive = FALSE)
## $ c.POSIXct:function (..., recursive = FALSE)
## $ c.POSIXlt:function (..., recursive = FALSE)
## $ c.warnings   :function (..., recursive = FALSE)

 .. --

and from these, only the 'noquote' method has a "\usage{ . }"
documentation.

The reason actually is that I had *wanted* to consider
__removing__ the 'recursive' argument from most of these S3 methods,
since all but  c.numeric_version()  completely disregard it and
it would be nicer if they did not have it.

HOWEVER, if it is removed and a user / code has

val <- c(, recursive = r)

then 'recursive' will become part of 'val' which is not desirable.

I had never thought more about this and if we should try or not to
remove it from the S3 methods in all those cases it is unused
... hoping that callers would also *not* set it.

As _one_ consequence I had decided rather *not* documenting it
for the S3 methods where it is (still ?!) part.

Martin

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Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

[Obenchain, Valerie]

Hi Roel,

Thank you for working on the package.

The builds start at 5pm EST daily. If it's helpful, you can see which R
version, compilers and compiler flags are used for each build machine by
clicking the name at the top left of the report:

http://www.bioconductor.org/checkResults/devel/bioc-LATEST/

Valerie



On 04/20/2017 12:38 AM, Janssen-10, R.R.E. wrote:
> Dear Valerie,
>
> We're working on MutationalPatterns as you can see (we've had our last 
> changes pushed into the SVN repository just two days ago).
> Due to the timezone differences between Europe and the US, we seem to be 
> missing out the starting point of a new build round.
>
> So, at which time do you start a new build round?  We have the fixes in place 
> to address the build issues.
> There seems to be a difference between the R setup on your build machines and 
> ours, which leads to differences in the tests.  They all pass on our 
> machines, so it's hard for us to debug this in a timely manner.
>
> Thanks!
>
> Kind regards,
> Roel Janssen
>
> 
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Obenchain, 
> Valerie [valerie.obench...@roswellpark.org]
> Sent: Wednesday, April 19, 2017 9:19 PM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] Bioconductor 3.5 release: potential deprecations
>
> Hi,
>
> Due to errors / unresponsive maintainers this new group of packages has
> been identified for potential deprecation in Biocondcutor 3.5.
>
> anamiR
> FunChiP
> MutationalPatterns
> seqplots
> snm
> ssviz
> stepwiseCM
> ToPASeq
>
> If anyone is interested in taking over as maintainer please let us know.
> If not fixed by Friday, April 21, these will be deprecated in 3.5.
>
> Valerie
>
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Re: [R-pkg-devel] How to fix errors in R headers when uploading my package to win-builer

[GSC]

I figured it out as header clash. Putting #include R headers after Windows
headers works for me.

GSC 于2017年4月18日周二 上午9:54写道：

> That link is deprecated, new link to log:
> https://win-builder.r-project.org/I3u4Z9BbLHsC/ .
>
> GSC 于2017年4月17日周一 下午10:47写道：
>
>> I have no idea how I could fix these compiling errors in R headers.
>> Testing my package locally on archlinux is fine. The link to build log is:
>> https://win-builder.r-project.org/08H2Ne0lShbY/ . Please help.
>>
>> Thanks!
>>
>

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Re: [Rd] R 3.4 has broken C++11 support

[Angerer, Philipp via R-devel]

indeed. Makeconf isn’t in the right spot, so the correct vars aren’t set. 

thank you all and sorry for the noise! 


Von: "Ista Zahn"  
An: "Angerer, Philipp"  
CC: "Dirk Eddelbuettel" , "Martyn Plummer" , 
"r-devel"  
Gesendet: Mittwoch, 19. April 2017 19:10:20 
Betreff: Re: [Rd] R 3.4 has broken C++11 support 

Hi Philipp, 

Fellow Archlinux user here. I think the problem is with the r-devel 
PKGBUILD file, rather than anything wrong in R itself. The PKGBUILD 
file does this: 

ln -s /etc/R/${i} ${i} 

when it should do 

ln -s /etc/R-devel/${i} ${i} 

You can fix your installed version with 

cd /opt/r-devel/lib/R/etc/ 
sudo rm ./* 
sudo ln -s /etc/R-devel/javaconf 
sudo ln -s /etc/R-devel/ldpaths 
sudo ln -s /etc/R-devel/Makeconf 
sudo ln -s /etc/R-devel/Renviron 
sudo ln -s /etc/R-devel/repositories 

Or (better) fix the PKGBUILD and makepkg/pacman -U 

Best, 
Ista 



On Wed, Apr 19, 2017 at 10:32 AM, Angerer, Philipp via R-devel 
 wrote: 
> Hi Dirk and Martyn, 
> 
>> That looks fine. Can you please give a reproducible example of a package 
>> that compiles correctly on R 3.3.3 but not with R 3.4.0 or R-devel. 
> 
> here you go, it’s pretty much the simplest package possible that needs C++11: 
> 
> https://github.com/flying-sheep/cxx11test 
> 
>> Maybe you can share with us how you configure the build of R-devel? 
> 
> Sure, in the mail you quoted, I already linked exactly that: 
> 
> https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=r-devel#n40 
> 
>> ./configure --prefix=/opt/r-devel \ 
>> --libdir=/opt/r-devel/lib \ 
>> --sysconfdir=/etc/R-devel \ 
>> --datarootdir=/opt/r-devel/share \ 
>> rsharedir=/opt/r-devel/share/R/ \ 
>> rincludedir=/opt/r-devel/include/R/ \ 
>> rdocdir=/opt/r-devel/share/doc/R/ \ 
>> --with-x \ 
>> --enable-R-shlib \ 
>> --with-lapack \ 
>> --with-blas \ 
>> F77=gfortran \ 
>> LIBnn=lib 
> 
> 
> Thanks and cheers, 
> Philipp 
> 
> 
> Helmholtz Zentrum Muenchen 
> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) 
> Ingolstaedter Landstr. 1 
> 85764 Neuherberg 
> www.helmholtz-muenchen.de 
> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe 
> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons 
> Enhsen 
> Registergericht: Amtsgericht Muenchen HRB 6466 
> USt-IdNr: DE 129521671 
> 
> __ 
> R-devel@r-project.org mailing list 
> https://stat.ethz.ch/mailman/listinfo/r-devel 

 


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Ingolstaedter Landstr. 1

85764 Neuherberg

www.helmholtz-muenchen.de

Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe

Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen

Registergericht: Amtsgericht Muenchen HRB 6466

USt-IdNr: DE 129521671


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Re: [Rd] ask.yes.no() function

[Michael Sumner]

Perhaps worth pointing out "yesno" as a candidate:


https://CRAN.R-project.org/package=yesno


Cheers, Mike



On Wed, 19 Apr 2017 at 21:55 Duncan Murdoch 
wrote:

As described in
, R base
functions are currently inconsistent in asking interactive "yes/no" type
questions. One solution to this is to have a function to do it, and to
use it consistently.




Rather than just writing such a function and possibly missing some
desirable feature, I'd like to ask if anyone can point to an existing
one that is perfect (or nearly perfect, and point out what changes would
be desirable)?

Duncan Murdoch

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Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

[Martin Morgan]

On 04/20/2017 03:08 AM, Michael Stadler wrote:

Dear Martin,

I've now spend a day trying to resolve this. To make a long story short:
I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile
and work under macOS Sierra.

I tried updating bowtie, but:
- bowtie 1.2 has a bug that prevents it from using multiple threads,
which I could reproduce both under Linux and macOS Sierra and which I
could not resolve (see https://github.com/BenLangmead/bowtie/issues/41).
- bowtie 1.1.2 crashes if compiled with clang (see
https://github.com/BenLangmead/bowtie/issues/21), the only known
workaround being to use a different toolchain, which I think is not an
option for BioC/Rbowtie.

I hope that resolves also the issue on El Capitan.


Thanks, it seems like the best available solution. Martin



Michael

On 19.04.2017 13:47, Martin Morgan wrote:

On 04/19/2017 05:45 AM, Michael Stadler wrote:

Dear BioC core,

Thanks for the report, Herve. If I understand correctly, there is
nothing I can do at this point to make QuasR green on windows, correct?

I have another question regarding QuasR not building on veracruz2: The
vignette does not build currently, reporting:
Error on veracruz2.bioconductor.org processing sample
/tmp/RtmpJBWrjI/chip_1_1.fq.bz2df0b6901ff33.fastq : 'asBam' internal:
samtools invoked 'abort' ...

Though it seems to build fine on other platforms, and there were no
recent changes to the vignette. What would you or other suggest to do
about that?


The error is in createGenomicAlignmentsController after

https://github.com/Bioconductor-mirror/QuasR/blob/cc374678033055f2bd4d105c502a426807223c1c/R/createAlignments-functions.R#L292


it looks like the sam file is quite funky

Browse[4]> options(nwarnings=1)
Browse[4]> xx = readLines(samFile)
There were 2339 warnings (use warnings() to see them)
Browse[4]> head(warnings(), 3)
Warning messages:
1: In readLines(samFile) : line 7 appears to contain an embedded nul
2: In readLines(samFile) : line 8 appears to contain an embedded nul
3: In readLines(samFile) : line 9 appears to contain an embedded nul
Browse[4]> table(nzchar(xx))

FALSE  TRUE
 2341   261
Browse[4]> substring(head(xx, 10), 1, 70)
 [1] "@HD\tVN:1.0\tSO:unsorted"
 [2] "@SQ\tSN:chr1\tLN:4"
 [3] "@SQ\tSN:chr2\tLN:1"
 [4] "@SQ\tSN:chr3\tLN:45000"
[5]
"@PG\tID:Bowtie\tVN:1.1.1\tCL:\"/Library/Frameworks/R.framework/Versions/3."

 [6] ""
 [7] ""
 [8] ""
 [9] ""
[10] ""

The 'abort' from Rsamtools is

  Parse error at line 143: missing colon in auxiliary data

It's not really clear whether R is being confused by the embedded nulls
or blank lines or other problem

Browse[4]> xx[140 + 1:5]
[1] "" "" "" "" ""
Browse[4]> xx[nzhchar(xx)][140 + 1:5]
Error in nzhchar(xx) : could not find function "nzhchar"
Browse[4]> xx[nzchar(xx)][140 + 1:5]
[1]
"seq10137\t4\t*\t0\t0\t*\t*\t0\t0\tTCGTTATGGTTTCCGTTGCTGCCATCTCACAT\tB@BABCBBBABABA?A>8>A7:6=@>>:@BAA>1;B\tXM:i:0"

[2]
"seq10138\t4\t*\t0\t0\t*\t*\t0\t0\tCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTC\tABBB@CBBBA9BB@>'>9@AA=A?\tXM:i:0"

[3]
"seq10139\t4\t*\t0\t0\t*\t*\t0\t0\tCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAAT\tBBCBBC=A@BAABBABBA=A??><\tXM:i:0"

[4]
"seq10140\t4\t*\t0\t0\t*\t*\t0\t0\tGGTTGTCAGCGTCATAAGAGGACCTCCAAATG\t;;;AA=AA>=CCBB>9@@>B=BB=\tXM:i:0"

[5]
"seq10141\t4\t*\t0\t0\t*\t*\t0\t0\tAACCCTAATGAGCTTAATCAAGATGATGCTCGTTAT\tBBAB@AAB@BBBA@B@ABAABBABAA@B?A?@\tXM:i:0"


So I guess it's in creation of the sam file -- Bowtie?

Martin



Any suggestions are appreciated,
Michael



On 17.04.2017 02:08, Hervé Pagès wrote:

FWIW here are all the packages that are victim of this
installed.packages bug in today's build report:

  alpine
  fCI
  GenomicFeatures
  QuasR

We only see this error on tokay2 (Windows).

H.


On 04/11/2017 04:21 PM, Gordon K Smyth wrote:

I restarted my PC this morning and the problem disappeared.

I probably should have tried that last night, but it was late ...

Thanks
Gordon


-Original Message-
From: Martin Morgan [mailto:martin.mor...@roswellpark.org]
Sent: Tuesday, 11 April 2017 7:20 PM
To: Gordon K Smyth ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

On 04/11/2017 05:01 AM, Gordon K Smyth wrote:

The problem appears to be with installed.packages(). If I start a
fresh R

3.4.0beta session, then I can run installed.packages() once with
correct results,
but running it a second time gives the error message:



installed.packages()

Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib)
&&  :
  missing value where TRUE/FALSE needed


The test is in this code chunk, from utils/R/packages.R

 for(lib in lib.loc) {
 if(noCache) {
 ret0 <- .readPkgDesc(lib, fields)
 if(length(ret0)) retval <- rbind(retval, ret0)
 } else {
 ## Previously used URLencode for e.g. Windows paths with
drives
 ## This version works for very long file names.
 

Re: [R-pkg-devel] R CMD check not finding my vignettes

[Brian G. Peterson]

David,

I'd suggest creating a vignette for each of HTML and PDF, and including 
a source file that contains the common code.  e.g. have a pdf header and 
an html header file, and then include the 'main' Rmd as a child doc from 
each header Rmd.  This way R CMD build could build both pdf and html 
versions of the output.


Regards,

Brian

On 04/20/2017 03:38 AM, David Hugh-Jones wrote:

Hi Duncan,

Thank you very much for taking the time to look at this.

I tried rebuilding the tar file so as to include only the .Rmd files, not
the HTML files, in 'vignettes':

drwxr-xr-x  0 david  staff   0 20 Apr 09:21 huxtable/vignettes/

-rw-r--r--  0 david  staff1633  6 Apr 16:26
huxtable/vignettes/comparison.csv

-rw-r--r--  0 david  staff6697  6 Apr 14:44
huxtable/vignettes/design-principles.Rmd

-rw-r--r--  0 david  staff5521  6 Apr 14:30
huxtable/vignettes/huxreg.Rmd

-rw-r--r--  0 david  staff   20552  6 Apr 16:19
huxtable/vignettes/huxtable.Rmd

-rw-r--r--  0 david  staff  22 17 Mar 00:19
huxtable/vignettes/placeins-header.tex


But when I run R CMD check, I still get the same warning:

* checking package vignettes in ‘inst/doc’ ... WARNING

Package vignettes without corresponding PDF/HTML:

   ‘design-principles.Rmd’

   ‘huxreg.Rmd’

   ‘huxtable.Rmd’

So, the warning does not seem to be related to the presence of HTML files
in vignettes.

I also tried manually removing .Rmd files from inst/doc (leaving them only
in vignettes) but this still gave the same error.

My goal here is that for package-specific reasons, I would like both pdf
and HTML versions of my vignettes to be available (I am writing code that
prints HTML and LaTeX tables and want my users to have examples of how both
output formats work). This is why I build those files manually, and place
them in inst/doc.

Side comment: at the moment, I feel as if I am running through the
combinatorics of including and excluding files from vignettes and inst/doc,
without much insight into what I am doing. Would it be fair to say that the
current system is not very easy to comprehend?

Cheers,

David

On 19 April 2017 at 21:24, Duncan Murdoch  wrote:


On 19/04/2017 1:00 PM, David Hugh-Jones wrote:


Hi Uwe,

I'm not sure if you ever got my off-list message with my tarball or
subsequent messages. I can't send a tarball on-list - it gets rejected as
too large - but here is a dropbox link. If you could confirm receipt, that
would be extremely helpful!

https://www.dropbox.com/s/179jrm19kx9o7dz/huxtable_0.2.0.tar.gz?dl=0



Not sure if Uwe has had a chance to look, but I just ran R CMD check on
your tarball using the latest version of R-devel.  It reported the
following problems:

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘David Hugh-Jones ’

Found the following (possibly) invalid URLs:
  URL: http://cran.rstudio.com/web/packages/huxtable/index.html
From: README.md
CRAN URL not in canonical form
  Canonical CRAN.R-project.org URLs use https.

The URL for your package should be in the form

https://CRAN.R-project.org/package=huxtable

* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘multirow.rds’

I'm not sure where that file belongs, but not there.

* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘huxreg.html’, ‘huxtable.html’

Those files shouldn't be in the vignettes directory, they are products of
building the vignettes.  Only the source should normally be in the
vignettes directory.

* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignettes without corresponding PDF/HTML:
   ‘design-principles.Rmd’
   ‘huxreg.Rmd’
   ‘huxtable.Rmd’

I think this is the warning you were asking about.  If I look at just the
first of those files, I see that design-principles.Rmd exists in vignettes
and is set to produce PDF output (only the first output entry in the YAML
counts).  You also have a .html file in vignettes; it shouldn't be there.
In inst/doc, you have source, .html and .pdf versions of that file.

The warning isn't very helpful, but I think it is triggered by the fact
that you've got the .html file in your vignettes directory.  If I remove
everything but the source from that directory, and everything from the
inst/doc directory, then all the vignette warnings go away.

(I haven't traced through the code, but I think the warning may be
literally correct.  Since you had .html files that looked like vignette
outputs but weren't, you have vignettes without *corresponding* HTML. It
would have been nicer if it suggested how to fix this, but that vignette
code is quite tricky, because any file could be source, and any html, tex
or pdf file could be output.  At some point I may try to clean it up a bit
and then maybe the error messages will be less obscure.)

Duncan Murdoch



[[alternative HTML version deleted]]

Re: [R-pkg-devel] R CMD check not finding my vignettes

[David Hugh-Jones]

Hi Duncan,

Thank you very much for taking the time to look at this.

I tried rebuilding the tar file so as to include only the .Rmd files, not
the HTML files, in 'vignettes':

drwxr-xr-x  0 david  staff   0 20 Apr 09:21 huxtable/vignettes/

-rw-r--r--  0 david  staff1633  6 Apr 16:26
huxtable/vignettes/comparison.csv

-rw-r--r--  0 david  staff6697  6 Apr 14:44
huxtable/vignettes/design-principles.Rmd

-rw-r--r--  0 david  staff5521  6 Apr 14:30
huxtable/vignettes/huxreg.Rmd

-rw-r--r--  0 david  staff   20552  6 Apr 16:19
huxtable/vignettes/huxtable.Rmd

-rw-r--r--  0 david  staff  22 17 Mar 00:19
huxtable/vignettes/placeins-header.tex


But when I run R CMD check, I still get the same warning:

* checking package vignettes in ‘inst/doc’ ... WARNING

Package vignettes without corresponding PDF/HTML:

   ‘design-principles.Rmd’

   ‘huxreg.Rmd’

   ‘huxtable.Rmd’

So, the warning does not seem to be related to the presence of HTML files
in vignettes.

I also tried manually removing .Rmd files from inst/doc (leaving them only
in vignettes) but this still gave the same error.

My goal here is that for package-specific reasons, I would like both pdf
and HTML versions of my vignettes to be available (I am writing code that
prints HTML and LaTeX tables and want my users to have examples of how both
output formats work). This is why I build those files manually, and place
them in inst/doc.

Side comment: at the moment, I feel as if I am running through the
combinatorics of including and excluding files from vignettes and inst/doc,
without much insight into what I am doing. Would it be fair to say that the
current system is not very easy to comprehend?

Cheers,

David

On 19 April 2017 at 21:24, Duncan Murdoch  wrote:

> On 19/04/2017 1:00 PM, David Hugh-Jones wrote:
>
>> Hi Uwe,
>>
>> I'm not sure if you ever got my off-list message with my tarball or
>> subsequent messages. I can't send a tarball on-list - it gets rejected as
>> too large - but here is a dropbox link. If you could confirm receipt, that
>> would be extremely helpful!
>>
>> https://www.dropbox.com/s/179jrm19kx9o7dz/huxtable_0.2.0.tar.gz?dl=0
>>
>>
> Not sure if Uwe has had a chance to look, but I just ran R CMD check on
> your tarball using the latest version of R-devel.  It reported the
> following problems:
>
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: ‘David Hugh-Jones ’
>
> Found the following (possibly) invalid URLs:
>   URL: http://cran.rstudio.com/web/packages/huxtable/index.html
> From: README.md
> CRAN URL not in canonical form
>   Canonical CRAN.R-project.org URLs use https.
>
> The URL for your package should be in the form
>
> https://CRAN.R-project.org/package=huxtable
>
> * checking top-level files ... NOTE
> Non-standard file/directory found at top level:
>   ‘multirow.rds’
>
> I'm not sure where that file belongs, but not there.
>
> * checking files in ‘vignettes’ ... WARNING
> Files in the 'vignettes' directory newer than all files in 'inst/doc':
>   ‘huxreg.html’, ‘huxtable.html’
>
> Those files shouldn't be in the vignettes directory, they are products of
> building the vignettes.  Only the source should normally be in the
> vignettes directory.
>
> * checking package vignettes in ‘inst/doc’ ... WARNING
> Package vignettes without corresponding PDF/HTML:
>‘design-principles.Rmd’
>‘huxreg.Rmd’
>‘huxtable.Rmd’
>
> I think this is the warning you were asking about.  If I look at just the
> first of those files, I see that design-principles.Rmd exists in vignettes
> and is set to produce PDF output (only the first output entry in the YAML
> counts).  You also have a .html file in vignettes; it shouldn't be there.
> In inst/doc, you have source, .html and .pdf versions of that file.
>
> The warning isn't very helpful, but I think it is triggered by the fact
> that you've got the .html file in your vignettes directory.  If I remove
> everything but the source from that directory, and everything from the
> inst/doc directory, then all the vignette warnings go away.
>
> (I haven't traced through the code, but I think the warning may be
> literally correct.  Since you had .html files that looked like vignette
> outputs but weren't, you have vignettes without *corresponding* HTML. It
> would have been nicer if it suggested how to fix this, but that vignette
> code is quite tricky, because any file could be source, and any html, tex
> or pdf file could be output.  At some point I may try to clean it up a bit
> and then maybe the error messages will be less obscure.)
>
> Duncan Murdoch
>

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Re: [Rd] Default R-3.4.0 RC CXXFLAGS without -O2 on x86_64-linux-gnu with g++-5.4.0 causes WARNING from stl_list.h

[Martyn Plummer]

This is fixed in R-rc_2017-04-19_r72555.tar.gz

If you are affected by this issue then please test the RC tarball. This
is the last chance to detect problems (including those created by the
last-minute patch) before the release of R 3.4.0.

Martyn

On Wed, 2017-04-19 at 12:19 +, Neumann, Steffen wrote:
> Hi r-devel,
> 
> a recent install of R-3.4.0 RC (2017-04-13 r72510) 
> on Linux (Ubuntu 16.04.1 LTS) x86_64-linux-gnu 
> with g++ (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
> (see http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-N
> odeInfo.html for more) 
> results in CXXFLAGS not containing "-O2" as optimisation flag,
> there is only "   -Wall", while CFLAGS are happy with "-g -O2
> -Wall"
> 
> This has an influence in at least one place
> https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010733.html
> where we have WARNINGS in R CMD check from "Found ‘abort’, 
> possibly from ‘abort’ (C)" in packages xcms/mzR.
> The abort() call is not coming from XCMS, but rather 
> from the C++ code in the STL:
> 
>   [...]
>   # 1770 "/usr/include/c++/5/bits/stl_list.h"
>   void _M_check_equal_allocators(list& __x) {
>    if (_M_get_Node_allocator())
>      __builtin_abort();
>   }
> 
> If we compile with -O2 optimisation, this getting rid of 
> the abort() symbol, as shown 
> in https://github.com/sneumann/xcms/issues/150#issuecomment-293545521
> 
> Martin Morgan created a minimum example that shows that 
> the symbol is indeed deep down in the STL (see below and in:
> https://stat.ethz.ch/pipermail/bioc-devel/2017-April/010837.html )
> 
> This raises several questions:
> 
> 1) is there any way to avoid the WARNING / abort() inside 
>    the STL list implementation ? Or just live with it ?
> 
> 2) If not, is there a reason why the Bioconductor build farm 
>    Ubuntu machine is not using -O2 as default CXXFLAG ?
>    BioC admins are trying to have a vanilla R installation with
> defaults. 
>    According to Herve Pages, CXXFLAGS without -O2 is default 
>    since R-3.4 beta, but I don't know enough about the package 
>    build logic to point to a particular R commit. 
> 
> 3) I thought about cheating the system and add -O2 
>    in the package CXXFLAGS, but Martin Morgan 
>    recommends packages shouldn't mess and override system build
> defaults
>    to mask and paper over the actual issue having a nasty abort() 
>    lurking somewhere.
>    But I couldn't add PKG_CXXFLAGS=-O2 in first place, since that 
>    triggers the different WARNING that -O2 is not portable. 
> 
> => Any help and input would be highly appreciated. 
> 
> Thanks in advance, 
> yours,
> Steffen
> 
> 
> tmp.cpp by Martin Morgan (also in above linked mail thread)
> ---
> #include 
> 
> int foo(int argc, const char *argv[]) {
>  std::list l1, l2;
>  std::list::iterator it;
> 
>  it = l1.begin();
>  l1.splice (it, l2); // mylist1: 1 10 20 30 2 3 4
> 
>  return 0;
> }
> ---
> 
> Test with
> 
>    rm -f tmp.o && R CMD SHLIB tmp.cpp && nm tmp.o | grep abort
> 
> with compiler settings in ~/.R/Makevars with/without -O2 
> -
> CXXFLAGS = -g -O0
> -
> 
> 
> 
> 
> 
> --
> IPB HalleAG Massenspektrometrie &
> Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle                       +49 (0) 345 5582 - 0           
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> 
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Re: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

[Janssen-10, R.R.E.]

Dear Valerie,

We're working on MutationalPatterns as you can see (we've had our last changes 
pushed into the SVN repository just two days ago).
Due to the timezone differences between Europe and the US, we seem to be 
missing out the starting point of a new build round.

So, at which time do you start a new build round?  We have the fixes in place 
to address the build issues.
There seems to be a difference between the R setup on your build machines and 
ours, which leads to differences in the tests.  They all pass on our machines, 
so it's hard for us to debug this in a timely manner.

Thanks!

Kind regards,
Roel Janssen


From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Obenchain, 
Valerie [valerie.obench...@roswellpark.org]
Sent: Wednesday, April 19, 2017 9:19 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Bioconductor 3.5 release: potential deprecations

Hi,

Due to errors / unresponsive maintainers this new group of packages has
been identified for potential deprecation in Biocondcutor 3.5.

anamiR
FunChiP
MutationalPatterns
seqplots
snm
ssviz
stepwiseCM
ToPASeq

If anyone is interested in taking over as maintainer please let us know.
If not fixed by Friday, April 21, these will be deprecated in 3.5.

Valerie



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Re: [R-pkg-devel] Interplay between knitr() and View()

[Thierry Onkelinx]

Dear Roy,

In case you create a HTML vignette you can use datatable() from the DT
package. That creates a dynamic table in the output.

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2017-04-19 19:20 GMT+02:00 Roy Mendelssohn - NOAA Federal <
roy.mendelss...@noaa.gov>:

> Hi All:
>
> My package allows the user to search for information about the data
> available, and the information is returned in a dataframe. I had long been
> looking for a nice way to display the results  (the datasets' metadata),
> and wasn't too happy with anything until I tried the View() command,  which
> does exactly what I want.
>
> The problem is I can't seem to find a way to make View() and knitr() work
> nice together in creating the vignette. Given the way View() works I doubt
> there is a way,  but any suggestions of how I can show what the user will
> see when the given the command in the package from within my vignette?
>
> Thanks,
>
> -Roy
>
>
>
> **
> "The contents of this message do not reflect any position of the U.S.
> Government or NOAA."
> **
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK
> Jr.
>
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Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

[Michael Stadler]

Dear Martin,

I've now spend a day trying to resolve this. To make a long story short:
I could get bowtie 1.1.1 (currently used in Rbowtie 1.15.1) to compile
and work under macOS Sierra.

I tried updating bowtie, but:
- bowtie 1.2 has a bug that prevents it from using multiple threads,
which I could reproduce both under Linux and macOS Sierra and which I
could not resolve (see https://github.com/BenLangmead/bowtie/issues/41).
- bowtie 1.1.2 crashes if compiled with clang (see
https://github.com/BenLangmead/bowtie/issues/21), the only known
workaround being to use a different toolchain, which I think is not an
option for BioC/Rbowtie.

I hope that resolves also the issue on El Capitan.

Michael

On 19.04.2017 13:47, Martin Morgan wrote:
> On 04/19/2017 05:45 AM, Michael Stadler wrote:
>> Dear BioC core,
>>
>> Thanks for the report, Herve. If I understand correctly, there is
>> nothing I can do at this point to make QuasR green on windows, correct?
>>
>> I have another question regarding QuasR not building on veracruz2: The
>> vignette does not build currently, reporting:
>> Error on veracruz2.bioconductor.org processing sample
>> /tmp/RtmpJBWrjI/chip_1_1.fq.bz2df0b6901ff33.fastq : 'asBam' internal:
>> samtools invoked 'abort' ...
>>
>> Though it seems to build fine on other platforms, and there were no
>> recent changes to the vignette. What would you or other suggest to do
>> about that?
> 
> The error is in createGenomicAlignmentsController after
> 
> https://github.com/Bioconductor-mirror/QuasR/blob/cc374678033055f2bd4d105c502a426807223c1c/R/createAlignments-functions.R#L292
> 
> 
> it looks like the sam file is quite funky
> 
> Browse[4]> options(nwarnings=1)
> Browse[4]> xx = readLines(samFile)
> There were 2339 warnings (use warnings() to see them)
> Browse[4]> head(warnings(), 3)
> Warning messages:
> 1: In readLines(samFile) : line 7 appears to contain an embedded nul
> 2: In readLines(samFile) : line 8 appears to contain an embedded nul
> 3: In readLines(samFile) : line 9 appears to contain an embedded nul
> Browse[4]> table(nzchar(xx))
> 
> FALSE  TRUE
>  2341   261
> Browse[4]> substring(head(xx, 10), 1, 70)
>  [1] "@HD\tVN:1.0\tSO:unsorted"
>  [2] "@SQ\tSN:chr1\tLN:4"
>  [3] "@SQ\tSN:chr2\tLN:1"
>  [4] "@SQ\tSN:chr3\tLN:45000"
> [5]
> "@PG\tID:Bowtie\tVN:1.1.1\tCL:\"/Library/Frameworks/R.framework/Versions/3."
> 
>  [6] ""
>  [7] ""
>  [8] ""
>  [9] ""
> [10] ""
> 
> The 'abort' from Rsamtools is
> 
>   Parse error at line 143: missing colon in auxiliary data
> 
> It's not really clear whether R is being confused by the embedded nulls
> or blank lines or other problem
> 
> Browse[4]> xx[140 + 1:5]
> [1] "" "" "" "" ""
> Browse[4]> xx[nzhchar(xx)][140 + 1:5]
> Error in nzhchar(xx) : could not find function "nzhchar"
> Browse[4]> xx[nzchar(xx)][140 + 1:5]
> [1]
> "seq10137\t4\t*\t0\t0\t*\t*\t0\t0\tTCGTTATGGTTTCCGTTGCTGCCATCTCACAT\tB@BABCBBBABABA?A>8>A7:6=@>>:@BAA>1;B\tXM:i:0"
> 
> [2]
> "seq10138\t4\t*\t0\t0\t*\t*\t0\t0\tCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTC\tABBB@CBBBA9BB@>'>9@AA=A?\tXM:i:0"
> 
> [3]
> "seq10139\t4\t*\t0\t0\t*\t*\t0\t0\tCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAAT\tBBCBBC=A@BAABBABBA=A??><\tXM:i:0"
> 
> [4]
> "seq10140\t4\t*\t0\t0\t*\t*\t0\t0\tGGTTGTCAGCGTCATAAGAGGACCTCCAAATG\t;;;AA=AA>=CCBB>9@@>B=BB=\tXM:i:0"
> 
> [5]
> "seq10141\t4\t*\t0\t0\t*\t*\t0\t0\tAACCCTAATGAGCTTAATCAAGATGATGCTCGTTAT\tBBAB@AAB@BBBA@B@ABAABBABAA@B?A?@\tXM:i:0"
> 
> 
> So I guess it's in creation of the sam file -- Bowtie?
> 
> Martin
> 
>>
>> Any suggestions are appreciated,
>> Michael
>>
>>
>>
>> On 17.04.2017 02:08, Hervé Pagès wrote:
>>> FWIW here are all the packages that are victim of this
>>> installed.packages bug in today's build report:
>>>
>>>   alpine
>>>   fCI
>>>   GenomicFeatures
>>>   QuasR
>>>
>>> We only see this error on tokay2 (Windows).
>>>
>>> H.
>>>
>>>
>>> On 04/11/2017 04:21 PM, Gordon K Smyth wrote:
 I restarted my PC this morning and the problem disappeared.

 I probably should have tried that last night, but it was late ...

 Thanks
 Gordon

> -Original Message-
> From: Martin Morgan [mailto:martin.mor...@roswellpark.org]
> Sent: Tuesday, 11 April 2017 7:20 PM
> To: Gordon K Smyth ; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta
>
> On 04/11/2017 05:01 AM, Gordon K Smyth wrote:
>> The problem appears to be with installed.packages(). If I start a
>> fresh R
> 3.4.0beta session, then I can run installed.packages() once with
> correct results,
> but running it a second time gives the error message:
>>
>>> installed.packages()
>> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib)
>> &&  :
>>   missing value where TRUE/FALSE needed
>
> The test is in this code chunk, from utils/R/packages.R
>
>  for(lib in lib.loc) {
>