Likun Wang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DEGseq |
| Branch: master |
| Last Commit: d6b7123 |
| Last Changed Date: 2018-12-03 06:32:19 -0400 (Mon, 03 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:57:37 -0400 (Tue, 09 Apr 2019).
| Package 402/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DEGseq 1.37.1 Likun Wang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: DEGseq |
| Version: 1.37.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DEGseq_1.37.1.tar.gz |
| StartedAt: 2019-04-09 02:11:38 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:12:49 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 71.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DEGseq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DEGseq_1.37.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DEGseq.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DEGseq/DESCRIPTION' ... OK
* this is package 'DEGseq' version '1.37.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DEGseq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.2Mb
sub-directories of 1Mb or more:
extdata 5.3Mb
libs 1.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'methods' 'qvalue'
Please remove these calls from your code.
Package in Depends field not imported from: 'qvalue'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEGexp: no visible global function definition for 'dev.cur'
DEGexp2: no visible global function definition for 'dev.cur'
getQvalue2: no visible global function definition for 'qvalue'
Undefined global functions or variables:
dev.cur qvalue
Consider adding
importFrom("grDevices", "dev.cur")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/DEGseq/libs/i386/DEGseq.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/DEGseq/libs/x64/DEGseq.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/DEGseq.Rcheck/00check.log'
for details.
DEGseq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DEGseq_1.37.1.tar.gz && rm -rf DEGseq.buildbin-libdir && mkdir DEGseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEGseq.buildbin-libdir DEGseq_1.37.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DEGseq_1.37.1.zip && rm DEGseq_1.37.1.tar.gz DEGseq_1.37.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1607k 100 1607k 0 0 16.8M 0 --:--:-- --:--:-- --:--:-- 18.2M
install for i386
* installing *source* package 'DEGseq' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getGeneExp.cpp -o getGeneExp.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o DEGseq.dll tmp.def getGeneExp.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DEGseq.buildbin-libdir/00LOCK-DEGseq/00new/DEGseq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DEGseq'
finding HTML links ... done
DEGexp html
DEGexp2 html
DEGseq html
GeneExpExample1000 html
GeneExpExample5000 html
getGeneExp html
kidneyChr21.bed html
kidneyChr21Bowtie html
liverChr21.bed html
liverChr21Bowtie html
readGeneExp html
refFlatChr21 html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'DEGseq' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c getGeneExp.cpp -o getGeneExp.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o DEGseq.dll tmp.def getGeneExp.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/DEGseq.buildbin-libdir/DEGseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEGseq' as DEGseq_1.37.1.zip
* DONE (DEGseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DEGseq' successfully unpacked and MD5 sums checked
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DEGseq.Rcheck/examples_i386/DEGseq-Ex.timings
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DEGseq.Rcheck/examples_x64/DEGseq-Ex.timings
|