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CHECK report for casper on merida2

This page was generated on 2019-04-09 13:27:50 -0400 (Tue, 09 Apr 2019).

Package 210/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
casper 2.17.1
David Rossell
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/casper
Branch: master
Last Commit: fd2e59a
Last Changed Date: 2019-01-04 13:21:12 -0400 (Fri, 04 Jan 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: casper
Version: 2.17.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:casper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings casper_2.17.1.tar.gz
StartedAt: 2019-04-08 23:40:48 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:46:26 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 337.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: casper.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:casper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings casper_2.17.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/casper.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.17.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘casper’ can be installed ... WARNING
Found the following significant warnings:
  seppel.cpp:484:2: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete]
  Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:47: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:54: unknown macro '\item'
  Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:58: unknown macro '\item'
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/casper.Rcheck/00install.out’ for details.
* 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 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 sizes of PDF files under ‘inst/doc’ ... 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/casper.Rcheck/00check.log’
for details.



Installation output

casper.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL casper
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘casper’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c casper.cpp -o casper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cstat.cpp -o cstat.o
cstat.cpp:16:19: warning: unused variable 'interface_c_sccs_id' [-Wunused-const-variable]
static const char interface_c_sccs_id[] = "%W%";
                  ^
cstat.cpp:17:19: warning: unused variable 'mess_c_sccs_id' [-Wunused-const-variable]
static const char mess_c_sccs_id[] = "%W%";
                  ^
cstat.cpp:18:19: warning: unused variable 'nrutil_c_sccs_id' [-Wunused-const-variable]
static const char nrutil_c_sccs_id[] = "%W%"; 
                  ^
cstat.cpp:19:19: warning: unused variable 'vector_c_sccs_id' [-Wunused-const-variable]
static const char vector_c_sccs_id[] = "%W%";
                  ^
cstat.cpp:20:19: warning: unused variable 'rand_c_sccs_id' [-Wunused-const-variable]
static const char rand_c_sccs_id[] = "@(#)$Workfile: rand.c$ $Revision: 5$";
                  ^
cstat.cpp:21:19: warning: unused variable 'cstat_c_sccs_id' [-Wunused-const-variable]
static const char cstat_c_sccs_id[] = "@(#)$Workfile: cstat.c$ $Revision: 2011-08-23$";
                  ^
6 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dataframe.cpp -o dataframe.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c discretedf.cpp -o discretedf.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dropVariant.cpp -o dropVariant.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c exon.cpp -o exon.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fragFunc.c -o fragFunc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fragment.cpp -o fragment.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c functions.c -o functions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hash.c -o hash.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c join_exons.c -o join_exons.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c makeIslands.c -o makeIslands.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c model.cpp -o model.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c model_cmp.cpp -o model_cmp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pathCounts.c -o pathCounts.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c procBam.c -o procBam.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rcasper.cpp -o rcasper.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c seppel.cpp -o seppel.o
seppel.cpp:484:2: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete]
        delete [] possiblemodels;
        ^     ˜˜˜
seppel.cpp:402:36: note: allocated with 'new' here
  vector<Model*>* possiblemodels = new vector<Model*>();
                                   ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c simReads.c -o simReads.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c simReadsfunc.c -o simReadsfunc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c smartmodeldist.cpp -o smartmodeldist.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c uniqQname.c -o uniqQname.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c variant.cpp -o variant.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c variant_cmp.cpp -o variant_cmp.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:47: unknown macro '\item'
Warning: /Users/biocbuild/bbs-3.9-bioc/meat/casper/man/getDistrs.Rd:54: unknown macro '\item'
Warning: /Users/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
* DONE (casper)

Tests output


Example timings

casper.Rcheck/casper-Ex.timings

nameusersystemelapsed
K562.r1l10.2480.0100.261
annotatedGenome-class0.0010.0000.002
asymmetryCheck0.0370.0010.039
calcDenovo000
calcExp3.2730.4833.796
denovoExpr4.2240.5434.808
denovoGeneExpr-class0.0010.0000.002
denovoGenomeExpr-class0.0000.0000.001
distrsGSE377040.2010.0130.222
genePlot0.3240.0310.360
getDistrs0.4880.0220.515
getIsland0.1090.0050.116
getNreads000
getReads000
getRoc000
hg19DB0.1070.0100.118
mergeBatches0.1020.0020.105
mergeExp0.0000.0000.001
modelPrior0.4930.0180.520
modelPriorAS-class0.0010.0000.000
pathCounts-class0.0010.0000.001
pathCounts000
plot-methods0.0000.0000.001
plotExpr000
plotPriorAS0.0000.0000.001
probNonEquiv0.1260.0040.135
procBam-class0.0010.0010.001
procBam000
procGenome0.0000.0010.001
qqnormGenomeWide0.0870.0030.094
quantileNorm0.0130.0020.015
relexprByGene0.0000.0000.001
rmShortInserts0.0010.0010.000
simMAE0.0010.0000.000
simMAEcheck000
simMultSamples000
simReads0.4540.0180.478
simulatedSamples-class0.0010.0000.002
splitGenomeByLength0.0000.0010.000
transcripts0.1690.0060.177
wrapDenovo0.0010.0000.000
wrapKnown0.0000.0010.001