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BioC 3.5: CHECK report for QuasR on malbec2

This page was generated on 2017-10-18 14:15:01 -0400 (Wed, 18 Oct 2017).

Package 1045/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.16.0
Michael Stadler
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/QuasR
Branch: RELEASE_3_5
Last Commit: 9ea8bf9
Last Changed Date: 2017-09-01 01:16:35 -0400 (Fri, 01 Sep 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QuasR
Version: 1.16.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings QuasR_1.16.0.tar.gz
StartedAt: 2017-10-18 01:45:24 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:57:12 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 707.8 seconds
RetCode: 0
Status:  OK 
CheckDir: QuasR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings QuasR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/QuasR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QuasR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuasR’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘QuasR’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.ShortReadQQA’ ‘ShortRead:::.qa_adapterContamination’
  ‘ShortRead:::.set_omp_threads’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
test: no visible global function definition for ‘defineTestSuite’
test: no visible global function definition for ‘runTestSuite’
test: no visible global function definition for ‘printTextProtocol’
Undefined global functions or variables:
  defineTestSuite printTextProtocol runTestSuite
* 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 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
qCount         7.508  0.256  24.844
qMeth          1.292  0.224  15.965
qExportWig     0.756  0.020  13.043
qProject-class 0.388  0.100  12.174
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘QuasR_unit_tests.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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/QuasR.Rcheck/00check.log’
for details.


QuasR.Rcheck/00install.out:

* installing *source* package ‘QuasR’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c cat_bam.c -o cat_bam.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c count_alignments.c -o count_alignments.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c count_alignments_subregions.c -o count_alignments_subregions.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c count_junctions.cpp -o count_junctions.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c export_wig.c -o export_wig.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c idxstats_bam.c -o idxstats_bam.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c profile_alignments.c -o profile_alignments.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c quantify_methylation.cpp -o quantify_methylation.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c split_sam_chr.c -o split_sam_chr.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o QuasR.so R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o /home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/QuasR.Rcheck/QuasR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (QuasR)

QuasR.Rcheck/QuasR-Ex.timings:

nameusersystemelapsed
QuasR-package000
alignmentStats0.0000.0000.001
preprocessReads2.4520.0002.456
qAlign000
qCount 7.508 0.25624.844
qExportWig 0.756 0.02013.043
qMeth 1.292 0.22415.965
qProfile0.7080.0080.719
qProject-class 0.388 0.10012.174
qQCReport2.2520.0682.324