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Rbowtie2 #457

Closed wzthu closed 7 years ago

wzthu commented 7 years ago

(Sorry, I over-wrote the original body opening this issue).

bioc-issue-bot commented 7 years ago

Hi @wzthu

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: Rbowtie2
Type: Package
Title: An R Wrapper for Bowtie2 and AdapterRemoval 
Version: 0.99.0
Date: 2017-08-18
Author: Zheng Wei, Wei Zhang
Maintainer: Zheng Wei <wzweizheng@qq.com>
Description:This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging.
License: GPL (>= 3)
Imports: Rcpp (>= 0.12.11)
Suggests: knitr
LinkingTo: Rcpp
SystemRequirements: C++11
Archs: x64
RoxygenNote: 6.0.1
biocViews: Sequencing, Alignment, Preprocessing
VignetteBuilder: knitr
bioc-issue-bot commented 7 years ago

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170824114606.html

wzthu commented 7 years ago

Deer reviewer,

There are two distinct errors from various OS/arch:

The first error is in R CMD BiocCheck: " Checking for bioc-devel mailing list subscription... * ERROR: Maintainer must subscribe to the bioc-devel mailing list. Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel " I subscribed just now and I think I have solved it.

The second error is in R CMD check, which is caused by architecture problem.

Because bowtie2 can only be compiled by 64bit g++ compiler, the compiler from mingw_32 etc. will cause errors. Therefore, Setting the arguments "--arch x64" and "--no-multiarch"
may be necessary for this package: "R --arch x64 CMD check --no-multiarch" And, I had declared “Arch: x64” in DESCRIPTION before I submmited.

Thanks!

Zheng Wei

魏征

------------------ Original ------------------ From: "bioc-issue-bot";notifications@github.com; Date: Thu, Aug 24, 2017 11:46 PM To: "Bioconductor/Contributions"Contributions@noreply.github.com; Cc: "魏征"wzweizheng@qq.com; "Mention"mention@noreply.github.com; Subject: Re: [Bioconductor/Contributions] Rbowtie2 (#457)

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170824114606.html

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bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

940ad23 change version to Version: 0.99.1

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, TIMEOUT, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170824232232.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

a6efbf5 support compiling with mingw32

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, TIMEOUT". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170825102653.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

99034e4 retry whether timeout

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170825212154.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

5bceb17 replace shared library with binary remove Rcpp re...

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

42a4a1e fix make clean bug in bowtie2 makefile

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170903133649.html

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170903135038.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

23a6a8f fix some bugs in Makefile

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170904052505.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

7186d8b fix some bugs in makefile

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170904063245.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

2832eab version bump

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170905021944.html

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

b9984d2 fix shared library required for Mac

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170905042618.html

LiNk-NY commented 7 years ago

Hi Zheng, @wzthu Thank you for your submission.

I apologize for the late response. I will be reviewing your package shortly.

Best regards, Marcel

wzthu commented 7 years ago

Thank you, @LiNk-NY. I am looking forward to your suggestion.

LiNk-NY commented 7 years ago

Hi Zheng, @wzthu I wasn't able to install the package locally. I'm not sure why. The build system installs the package without a problem.

You will get the review shortly. Thanks.

Regards, Marcel

less Rbowtie2.Rcheck/00install.out

* installing *source* package ‘Rbowtie2’ ...
** libs
** arch - 
mkdir -p ../inst
(cd adapterremoval && (make -j8 CXX="g++ -std=gnu++11" -f Makefile))
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: Entering directory '/home/mramos/Documents/Bioconductor/GitHub/Rbowtie2.Rcheck/00_pkg_src/Rbowtie2/src/adapterremoval'
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c adapterset.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c alignment.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c argparse.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c debug.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c demultiplex.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq_enc.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq_io.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c linereader.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c linereader_joined.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_adapter_id.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_adapter_rm.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_demultiplex.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c scheduler.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c strutils.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c threads.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c timer.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c trimmed_reads.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c userconfig.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main.cc 
cp AdapterRemoval ../../inst/
cp: cannot stat 'AdapterRemoval': No such file or directory
Makefile:50: recipe for target 'install' failed
make[1]: *** [install] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/home/mramos/Documents/Bioconductor/GitHub/Rbowtie2.Rcheck/00_pkg_src/Rbowtie2/src/adapterremoval'
Makefile:9: recipe for target 'all' failed
make: *** [all] Error 2
ERROR: compilation failed for package ‘Rbowtie2’
* removing ‘/home/mramos/Documents/Bioconductor/GitHub/Rbowtie2.Rcheck/Rbowtie2’
LiNk-NY commented 7 years ago

Hi Zheng, @wzthu Thank you for submitting to Bioconductor!

Please see your package review below.

Feel free to contact me if you have any questions.

Best regards, Marcel

Rbowtie2 #457

The Rbowtie2 does not import any Bioconductor packages. We can see that an R interface to bowtie2 is valuable but it does not make an attempt to integrate to the Bioconductor infrastructure. I will discuss this with the Bioconductor core team and I will get back to you.

DESCRIPTION

R

vignettes

bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

b834871 fix bugs that makefile does not support multicore ... 0e4295f add depends of R 304dad7 fix make clean bug 0b91b51 add session info and rewrite the scripts that prin... 6848642 revise the annotations and parameters in functions a24c0c4 rewrite 1 :length(x)) with seq_along(x) 35604a3 rewrite paramArray<-c() d4c577e version bump

bioc-issue-bot commented 7 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/Rbowtie2_buildreport_20170916002649.html

wzthu commented 7 years ago

Thank you for your suggestions, Marcel @LiNk-NY .

You mentioned that you were not able to install the package locally.

That is because we did not consider multi-core compiling for Makefiles.

We have revised the Makefiles to fix this bug.

Besides, we have revised the related problem according to package review.

LiNk-NY commented 7 years ago

Hi Zheng, @wzthu Thank you for making those changes! Your package has been accepted. Thank you for submitting to Bioconductor.

Best regards, Marcel

bioc-issue-bot commented 7 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!

wzthu commented 7 years ago

Great! Thanks, Marcel @LiNk-NY !

mtmorgan commented 7 years ago

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