[Bioc-devel] rJava on Windows builders

[Obenchain, Valerie]

Just a heads up that the new version of rJava that came out 5/29/2018 failed to 
install on the Windows builders yesterday. Because of this we see an increased 
number of failures in both release and devel. Unfortunately I didn't notice 
this before the builds started today so we'll see the same errors tomorrow.

This should be cleared up for the report that posts on Saturday, June 2.

Valerie


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Re: [Bioc-devel] onLoad failed for rJava in nigthly 'devel' build

[Obenchain, Valerie]

Hi Lulu,

Thanks for keeping an eye on the build report!

It looks like something went wrong when the new version of rJava was installed 
on the Windows builders yesterday. Unfortunately today's builds started before 
we realized this so your package will likely have the same error on tomorrow's 
report. We'll investigate and hopefully have this cleared up for the report 
that will post on Saturday.

Valerie


On 05/31/2018 11:43 AM, Lulu Chen wrote:

Dear Bioc Team,

My package "CAMTHC" has been accepted and  included in the nigthly 'devel'
build . However, build error appears in "Windows Server 2012 R2 Standard /
x64":

install for i386

* installing *source* package 'CAMTHC' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: library.dynam("rJava", pkgname, libname)
  error: DLL 'rJava' not found: maybe not installed for this architecture?
ERROR: lazy loading failed for package 'CAMTHC'
* removing
'C:/Users/biocbuild/bbs-3.8-bioc/meat/CAMTHC.buildbin-libdir/CAMTHC'
In R CMD INSTALL
In R CMD INSTALL

I only met this problem in my own computer before I set java correctly. All
advice I find online is about how to set java in your own computer. I
passed the build check at the Bioconductor Contributions repository. So
now,  could anyone help me to fix this problem in  'devel' build? Thanks!

Best,
Lulu

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[Bioc-devel] onLoad failed for rJava in nigthly 'devel' build

[Lulu Chen]

Dear Bioc Team,

My package "CAMTHC" has been accepted and  included in the nigthly 'devel'
build . However, build error appears in "Windows Server 2012 R2 Standard /
x64":

install for i386

* installing *source* package 'CAMTHC' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: library.dynam("rJava", pkgname, libname)
  error: DLL 'rJava' not found: maybe not installed for this architecture?
ERROR: lazy loading failed for package 'CAMTHC'
* removing
'C:/Users/biocbuild/bbs-3.8-bioc/meat/CAMTHC.buildbin-libdir/CAMTHC'
In R CMD INSTALL
In R CMD INSTALL

I only met this problem in my own computer before I set java correctly. All
advice I find online is about how to set java in your own computer. I
passed the build check at the Bioconductor Contributions repository. So
now,  could anyone help me to fix this problem in  'devel' build? Thanks!

Best,
Lulu

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

[Obenchain, Valerie]

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


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

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

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

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

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

Thank,
Mike

--

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

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

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

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

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

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

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Re: [Bioc-devel] build cache on bioconductor build system?

[Shepherd, Lori]

The single package builder has not built in the functionality to obey this 
particular BBSoption but should be active on the builder once officially 
accepted into Bioconductor.  Your reviewer will be aware of this and be able to 
proceed with the review.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Vivek Bhardwaj 

Sent: Thursday, May 31, 2018 11:13:52 AM
To: Herv� Pag�s; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] build cache on bioconductor build system?

The name of my package is icetea. Here's the link
 to the
submission. I checked today and VariantAnnotation build was passing now,
so simply re-pushed with bumped version and it worked! (well not
exactly, I still have the RSubread issue with windows that I mentioned
last week, but at least VariantAnnotation is not throwing errors).

@Herv� Regarding the issue with RSubread, I tried adding the .BBSoptions
file in the package source dir. Although I added this file under
.Rbuildignore as well to avoid R CMD check complaining about
non-standard dir. It didn't work.


Thanks for the input everyone.

Best,

Vivek



On 5/30/18 7:31 PM, Herv� Pag�s wrote:
> Hi Vivek,
>
> Are you submitting a package and bumped its version in order to trigger
> a new build? The build system used for the submission is the "Single
> Package Builder" (SPB) and is not the same as the main builder used
> for the daily builds (BBS). It would help if you could provide the link
> to the build report where you see the error or at least the name of
> your package.
>
> On 05/30/2018 07:30 AM, Vivek Bhardwaj wrote:
>>
>> The package throwing error is*VariantAnnotation *(coming from function:
>> locateVariants). I checked it's build for the dev branch and indeed it's
>> broken. **
>>
>> All right then I would remove version specification from my package and
>> I guess I'll wait for**VariantAnnotation to get fixed.
>
> FWIW the latest version of VariantAnnotation in devel is 1.27.1:
>
> https://bioconductor.org/packages/3.8/bioc/html/VariantAnnotation.html
>
> and it passes BUILD and CHECK today on all platforms today.
>
> The SPB sometimes needs to install dependencies that in some rare
> occasion can get stale a few days later. So in a sense yes it can
> cache packages. Lori, our SPB expert, will be able to help you with
> this if you provide the name of your package. Thanks!
>
> H.
>
>>
>> Best,
>> Vivek
>>
>>
>>
>> On 05/30/2018 04:04 PM, Martin Morgan wrote:
>>> There is no cache; like users you get the 'current' version of the
>>> package from the relevant repository. If your package used
>>> concatenateObjects, then it needs to be updated. If your package is
>>> broken through a third package, it needs to be fixed (perhaps it has
>>> been but did not propagate, see the build reports for packages in the
>>> devel branch
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XilqVN5SNnjEa4_siRsVQPa3EsNEK53OKM7n156DDnc&s=nghjJ8CDqIvM9dcgTCxhGrxP3XlnGhurWc5aREDAIyk&e=
>>> , and look for the
>>> stoplight at the right).
>>>
>>> Martin
>>>
>>> On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote:
 Hi All

 Is there any build cache on bioc build system? I updated S4Vector and
 IRanges in my dependencies and triggered a new build of my package,
 only
 to find that this broke other dependencies due to renaming of function
 `concatenateObjects ` to `bindRows` in S4Vector. Now I removed the
 mentioned versions in my DESCRIPTION, but the build is still broken.
 Also tried specifying a particular version of these packages and I get
 the error :

 ** byte-compile and prepare package for lazy loading Error in
 loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
 vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but ==
 2.14.10
 is required

 How do I refresh the cache?

>>>
>>>
>>> This email message may contain legally privileged and/or confidential
>>> information.  If you are not the intended recipient(s), or the
>>> employee or agent responsible for the delivery of this message to the
>>> intended recipient(s), you are hereby notified that any disclosure,
>>> copying, distribution, or use of this email message is prohibited.  If
>>> you have received this message in error, please notify the sender
>>> immediately by e-mail and delete this email message from your
>>> computer. Thank you.
>>
>>
>


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i

Re: [Bioc-devel] build cache on bioconductor build system?

[Vivek Bhardwaj]

The name of my package is icetea. Here's the link 
 to the 
submission. I checked today and VariantAnnotation build was passing now, 
so simply re-pushed with bumped version and it worked! (well not 
exactly, I still have the RSubread issue with windows that I mentioned 
last week, but at least VariantAnnotation is not throwing errors).

@Hervé Regarding the issue with RSubread, I tried adding the .BBSoptions 
file in the package source dir. Although I added this file under 
.Rbuildignore as well to avoid R CMD check complaining about 
non-standard dir. It didn't work.


Thanks for the input everyone.

Best,

Vivek



On 5/30/18 7:31 PM, Hervé Pagès wrote:
> Hi Vivek,
>
> Are you submitting a package and bumped its version in order to trigger
> a new build? The build system used for the submission is the "Single
> Package Builder" (SPB) and is not the same as the main builder used
> for the daily builds (BBS). It would help if you could provide the link
> to the build report where you see the error or at least the name of
> your package.
>
> On 05/30/2018 07:30 AM, Vivek Bhardwaj wrote:
>>
>> The package throwing error is*VariantAnnotation *(coming from function:
>> locateVariants). I checked it's build for the dev branch and indeed it's
>> broken. **
>>
>> All right then I would remove version specification from my package and
>> I guess I'll wait for**VariantAnnotation to get fixed.
>
> FWIW the latest version of VariantAnnotation in devel is 1.27.1:
>
> https://bioconductor.org/packages/3.8/bioc/html/VariantAnnotation.html
>
> and it passes BUILD and CHECK today on all platforms today.
>
> The SPB sometimes needs to install dependencies that in some rare
> occasion can get stale a few days later. So in a sense yes it can
> cache packages. Lori, our SPB expert, will be able to help you with
> this if you provide the name of your package. Thanks!
>
> H.
>
>>
>> Best,
>> Vivek
>>
>>
>>
>> On 05/30/2018 04:04 PM, Martin Morgan wrote:
>>> There is no cache; like users you get the 'current' version of the
>>> package from the relevant repository. If your package used
>>> concatenateObjects, then it needs to be updated. If your package is
>>> broken through a third package, it needs to be fixed (perhaps it has
>>> been but did not propagate, see the build reports for packages in the
>>> devel branch 
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=XilqVN5SNnjEa4_siRsVQPa3EsNEK53OKM7n156DDnc&s=nghjJ8CDqIvM9dcgTCxhGrxP3XlnGhurWc5aREDAIyk&e=
>>>  
>>> , and look for the
>>> stoplight at the right).
>>>
>>> Martin
>>>
>>> On 05/30/2018 09:56 AM, Vivek Bhardwaj wrote:
 Hi All

 Is there any build cache on bioc build system? I updated S4Vector and
 IRanges in my dependencies and triggered a new build of my package, 
 only
 to find that this broke other dependencies due to renaming of function
 `concatenateObjects ` to `bindRows` in S4Vector. Now I removed the
 mentioned versions in my DESCRIPTION, but the build is still broken.
 Also tried specifying a particular version of these packages and I get
 the error :

 ** byte-compile and prepare package for lazy loading Error in
 loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
 vI[[j]]) : namespace 'IRanges' 2.15.13 is already loaded, but == 
 2.14.10
 is required

 How do I refresh the cache?

>>>
>>>
>>> This email message may contain legally privileged and/or confidential
>>> information.  If you are not the intended recipient(s), or the
>>> employee or agent responsible for the delivery of this message to the
>>> intended recipient(s), you are hereby notified that any disclosure,
>>> copying, distribution, or use of this email message is prohibited.  If
>>> you have received this message in error, please notify the sender
>>> immediately by e-mail and delete this email message from your
>>> computer. Thank you.
>>
>>
>


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