SeqArray 1.16.0
Xiuwen Zheng
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/SeqArray | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SeqArray_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SeqArray.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SeqArray’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.6Mb
sub-directories of 1Mb or more:
doc 3.5Mb
extdata 1.6Mb
libs 3.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘SeqArray/libs/SeqArray.so’:
Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
‘R_WriteConnection’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/SeqArray.Rcheck/00check.log’
for details.
* installing *source* package ‘SeqArray’ ...
** libs
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c ConvToGDS.cpp -o ConvToGDS.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c FileMerge.cpp -o FileMerge.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c GetData.cpp -o GetData.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c Index.cpp -o Index.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c Methods.cpp -o Methods.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_SeqArray.c -o R_SeqArray.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c ReadBySample.cpp -o ReadBySample.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c ReadByVariant.cpp -o ReadByVariant.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c SeqArray.cpp -o SeqArray.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c pkg_test.cpp -o pkg_test.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I. -DUSING_R -I"/home/biocbuild/bbs-3.5-bioc/R/library/gdsfmt/include" -I/usr/local/include -fpic -g -O2 -Wall -c vectorization.c -o vectorization.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o vectorization.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/SeqArray.Rcheck/SeqArray/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SeqArray)