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CHECK report for casper on malbec2

This page was generated on 2019-10-16 12:02:15 -0400 (Wed, 16 Oct 2019).

Package 213/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
casper 2.18.0
David Rossell
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/casper
Branch: RELEASE_3_9
Last Commit: 1239f31
Last Changed Date: 2019-05-02 11:53:40 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: casper
Version: 2.18.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings casper_2.18.0.tar.gz
StartedAt: 2019-10-16 00:18:08 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:22:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 276.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: casper.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings casper_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/casper.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.18.0’
* 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 ‘casper’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /home/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:47: unknown macro '\item'
  Warning: /home/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:54: unknown macro '\item'
  Warning: /home/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:58: unknown macro '\item'
See ‘/home/biocbuild/bbs-3.9-bioc/meat/casper.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   3.2Mb
* 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 ... NOTE
.mergeFramesViaRanges: no visible global function definition for
  ‘queryHits’
.mergeFramesViaRanges: no visible global function definition for
  ‘subjectHits’
assignExons2GeneF: no visible global function definition for
  ‘queryHits’
assignExons2GeneF: no visible global function definition for
  ‘subjectHits’
findNewExonsF: no visible global function definition for ‘queryHits’
generateNOexons: no visible global function definition for ‘queryHits’
generateNOexons: no visible global function definition for
  ‘subjectHits’
getDistrsFromBam: no visible global function definition for
  ‘subjectHits’
getDistrsFromBam: no visible global function definition for ‘queryHits’
getDistrsFrompBam: no visible global function definition for
  ‘subjectHits’
getDistrsFrompBam: no visible global function definition for
  ‘queryHits’
procPaths: no visible global function definition for ‘queryHits’
procPaths: no visible global function definition for ‘subjectHits’
Undefined global functions or variables:
  queryHits subjectHits
* checking Rd files ... WARNING
prepare_Rd: man/getDistrs.Rd:47: unknown macro '\item'
prepare_Rd: man/getDistrs.Rd:54: unknown macro '\item'
prepare_Rd: man/getDistrs.Rd:58: unknown macro '\item'
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/casper.Rcheck/00check.log’
for details.



Installation output

casper.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL casper
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘casper’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c casper.cpp -o casper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c cstat.cpp -o cstat.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c dataframe.cpp -o dataframe.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c discretedf.cpp -o discretedf.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c dropVariant.cpp -o dropVariant.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c exon.cpp -o exon.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c fragFunc.c -o fragFunc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c fragment.cpp -o fragment.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c functions.c -o functions.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c join_exons.c -o join_exons.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c makeIslands.c -o makeIslands.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c model.cpp -o model.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c model_cmp.cpp -o model_cmp.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c pathCounts.c -o pathCounts.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c procBam.c -o procBam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c rcasper.cpp -o rcasper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c seppel.cpp -o seppel.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c simReads.c -o simReads.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c simReadsfunc.c -o simReadsfunc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c uniqQname.c -o uniqQname.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c variant.cpp -o variant.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c variant_cmp.cpp -o variant_cmp.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o casper.so casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-casper/00new/casper/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘transcripts’ in package ‘casper’
** help
Warning: /home/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:47: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:54: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:58: unknown macro '\item'
*** installing help indices
** building package indices
** installing vignettes
   ‘casper.Rnw’ 
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (casper)

Tests output


Example timings

casper.Rcheck/casper-Ex.timings

nameusersystemelapsed
K562.r1l10.2010.0400.241
annotatedGenome-class0.0010.0000.001
asymmetryCheck0.0120.0000.011
calcDenovo0.0010.0000.000
calcExp3.3190.0963.415
denovoExpr3.4080.1243.620
denovoGeneExpr-class0.0010.0000.000
denovoGenomeExpr-class000
distrsGSE377040.1660.0020.168
genePlot0.2260.0200.246
getDistrs0.3920.0480.441
getIsland0.0820.0000.083
getNreads0.0000.0000.001
getReads0.0010.0000.000
getRoc000
hg19DB0.080.000.08
mergeBatches0.0770.0000.078
mergeExp000
modelPrior0.3070.0040.326
modelPriorAS-class0.0010.0000.001
pathCounts-class000
pathCounts000
plot-methods0.0010.0000.000
plotExpr000
plotPriorAS000
probNonEquiv0.0940.0000.094
procBam-class000
procBam000
procGenome000
qqnormGenomeWide0.0550.0000.055
quantileNorm0.0110.0000.011
relexprByGene000
rmShortInserts000
simMAE000
simMAEcheck000
simMultSamples000
simReads0.3870.0360.423
simulatedSamples-class000
splitGenomeByLength000
transcripts0.1530.0000.152
wrapDenovo000
wrapKnown0.0000.0000.001