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CHECK report for casper on malbec2

This page was generated on 2018-10-17 08:24:52 -0400 (Wed, 17 Oct 2018).

Package 190/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
casper 2.14.0
David Rossell
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/casper
Branch: RELEASE_3_7
Last Commit: 1822e92
Last Changed Date: 2018-04-30 10:35:28 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: casper
Version: 2.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings casper_2.14.0.tar.gz
StartedAt: 2018-10-15 23:00:16 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:03:40 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 204.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: casper.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:casper.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings casper_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/casper.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.14.0’
* 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-3.7-bioc/meat/casper/man/getDistrs.Rd:47: unknown macro '\item'
  Warning: /home/biocbuild/bbs-3.7-bioc/meat/casper/man/getDistrs.Rd:54: unknown macro '\item'
  Warning: /home/biocbuild/bbs-3.7-bioc/meat/casper/man/getDistrs.Rd:58: unknown macro '\item'
See ‘/home/biocbuild/bbs-3.7-bioc/meat/casper.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
* 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: getDistrs.Rd:47: unknown macro '\item'
prepare_Rd: getDistrs.Rd:54: unknown macro '\item'
prepare_Rd: 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-3.7-bioc/meat/casper.Rcheck/00check.log’
for details.



Installation output

casper.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL casper
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘casper’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c casper.cpp -o casper.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c cstat.cpp -o cstat.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dataframe.cpp -o dataframe.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c discretedf.cpp -o discretedf.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c dropVariant.cpp -o dropVariant.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c exon.cpp -o exon.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fragFunc.c -o fragFunc.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fragment.cpp -o fragment.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c functions.c -o functions.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c makeIslands.c -o makeIslands.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c model.cpp -o model.o
g++  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pathCounts.c -o pathCounts.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c procBam.c -o procBam.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rcasper.cpp -o rcasper.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c seppel.cpp -o seppel.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c simReads.c -o simReads.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c simReadsfunc.c -o simReadsfunc.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c uniqQname.c -o uniqQname.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c variant.cpp -o variant.o
g++  -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c variant_cmp.cpp -o variant_cmp.o
g++ -shared -L/home/biocbuild/bbs-3.7-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-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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-3.7-bioc/meat/casper/man/getDistrs.Rd:47: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.7-bioc/meat/casper/man/getDistrs.Rd:54: unknown macro '\item'
Warning: /home/biocbuild/bbs-3.7-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
* DONE (casper)

Tests output


Example timings

casper.Rcheck/casper-Ex.timings

nameusersystemelapsed
K562.r1l10.1880.0320.226
annotatedGenome-class0.0000.0000.001
asymmetryCheck0.0200.0000.021
calcDenovo000
calcExp2.5120.0962.618
denovoExpr2.9520.1323.087
denovoGeneExpr-class0.0000.0000.001
denovoGenomeExpr-class0.0040.0000.002
distrsGSE377040.1480.0040.151
genePlot0.2680.0160.284
getDistrs0.3840.0440.426
getIsland0.0800.0000.081
getNreads000
getReads000
getRoc000
hg19DB0.0840.0000.082
mergeBatches0.0760.0000.077
mergeExp0.0040.0000.001
modelPrior0.3280.0040.341
modelPriorAS-class0.0000.0000.001
pathCounts-class0.0000.0000.001
pathCounts0.0040.0000.001
plot-methods0.0000.0000.001
plotExpr0.0040.0000.001
plotPriorAS0.0000.0000.001
probNonEquiv0.1720.0000.172
procBam-class0.0000.0000.001
procBam0.0000.0000.001
procGenome0.0000.0000.001
qqnormGenomeWide0.10.00.1
quantileNorm0.0160.0000.018
relexprByGene0.0000.0000.001
rmShortInserts0.0000.0000.001
simMAE0.0000.0000.001
simMAEcheck0.0040.0000.001
simMultSamples0.0000.0000.001
simReads0.5960.0440.642
simulatedSamples-class0.0000.0000.001
splitGenomeByLength000
transcripts0.1520.0000.154
wrapDenovo0.0040.0000.001
wrapKnown0.0000.0000.001