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This page was generated on 2015-11-10 14:47:54 -0800 (Tue, 10 Nov 2015).
| Package 141/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| casper 2.4.0 David Rossell
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS |  | |||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: casper |
| Version: 2.4.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings casper_2.4.0.tar.gz |
| StartedAt: 2015-11-10 02:53:45 -0800 (Tue, 10 Nov 2015) |
| EndedAt: 2015-11-10 02:59:32 -0800 (Tue, 10 Nov 2015) |
| EllapsedTime: 347.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: casper.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings casper_2.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/casper.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘casper/DESCRIPTION’ ... OK
* this is package ‘casper’ version ‘2.4.0’
* 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 ... [41s/42s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rangesPlot,IRanges-ANY : .local: warning in genePlot(gene = gene, xlab
= "", ylab = "", xlim = xlim, ...): partial argument match of 'gene'
to 'generanges'
rangesPlot,procBam-ANY : .local: warning in genePlot(gene = gene, xlab
= "", ylab = "", xlim = xlim, ...): partial argument match of 'gene'
to 'generanges'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'plot' and siglist 'readDistrsList,ANY'
generic 'procBam' and siglist 'ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getDistrs':
getDistrs
Code: function(DB, bam, pbam, islandid = NULL, verbose = FALSE,
nreads = 4 * 10^6, readLength, min.gt.freq = NULL,
tgroups = 5, mc.cores = 1)
Docs: function(DB, bam, pbam, islandid, verbose, nreads = 4 * 10^6,
readLength)
Argument names in code not in docs:
min.gt.freq tgroups mc.cores
Mismatches in argument default values:
Name: 'islandid' Code: NULL Docs:
Name: 'verbose' Code: FALSE Docs:
Codoc mismatches from documentation object 'procBam':
procBam
Code: function(bam, stranded = FALSE, seed = as.integer(1), verbose =
FALSE, rname = "null", keep.junx = FALSE, keep.flag =
FALSE, ispaired = TRUE, ...)
Docs: function(bam, stranded, seed, verbose = FALSE, rname, keep.junx
= FALSE, keep.flag = FALSE, ...)
Argument names in code not in docs:
ispaired
Mismatches in argument names:
Position: 8 Code: ispaired Docs: ...
Mismatches in argument default values:
Name: 'stranded' Code: FALSE Docs:
Name: 'seed' Code: as.integer(1) Docs:
Name: 'rname' Code: "null" Docs:
Codoc mismatches from documentation object 'simMAE':
simMAE
Code: function(nsim, islandid, nreads, readLength, fragLength, burnin
= 1000, pc, distr, readLength.pilot = readLength,
eset.pilot, usePilot = FALSE, retTxsError = FALSE,
genomeDB, mc.cores = 1, mc.cores.int = 1, verbose =
FALSE, writeBam = FALSE, bamFile = NULL)
Docs: function(nsim, islandid, nreads, readLength, fragLength, burnin
= 1000, pc, distr, readLength.pilot = readLength,
eset.pilot, usePilot = FALSE, retTxsError = FALSE,
genomeDB, mc.cores = 1, mc.cores.int = 1, verbose =
FALSE)
Argument names in code not in docs:
writeBam bamFile
* 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 ... [27s/29s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
denovoExpr 4.512 0.432 5.259
* 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-3.2-bioc/meat/casper.Rcheck/00check.log’
for details.
casper.Rcheck/00install.out:
* installing *source* package ‘casper’ ... ** libs llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c casper.cpp -o casper.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c cstat.cpp -o cstat.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c dataframe.cpp -o dataframe.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c discretedf.cpp -o discretedf.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c dropVariant.cpp -o dropVariant.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c exon.cpp -o exon.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c fragFunc.c -o fragFunc.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c fragment.cpp -o fragment.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c functions.c -o functions.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c hash.c -o hash.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c join_exons.c -o join_exons.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c makeIslands.c -o makeIslands.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c model.cpp -o model.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c model_cmp.cpp -o model_cmp.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c pathCounts.c -o pathCounts.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c procBam.c -o procBam.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c rcasper.cpp -o rcasper.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c seppel.cpp -o seppel.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c simReads.c -o simReads.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c simReadsfunc.c -o simReadsfunc.o simReadsfunc.c: In function ‘build_cigar’: simReadsfunc.c:279: warning: unused variable ‘rlb’ simReadsfunc.c:279: warning: unused variable ‘correct’ llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c smartmodeldist.cpp -o smartmodeldist.o llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c uniqQname.c -o uniqQname.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c variant.cpp -o variant.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c variant_cmp.cpp -o variant_cmp.o llvm-g++-4.2 -arch x86_64 -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 -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 /Users/biocbuild/bbs-3.2-bioc/meat/casper.Rcheck/casper/libs ** R ** data ** inst ** preparing package for lazy loading Creating a new generic function for ‘transcripts’ in package ‘casper’ Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘casper’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (casper)
casper.Rcheck/casper-Ex.timings:
| name | user | system | elapsed | |
| K562.r1l1 | 0.213 | 0.005 | 0.218 | |
| annotatedGenome-class | 0.001 | 0.000 | 0.003 | |
| asymmetryCheck | 0.025 | 0.001 | 0.026 | |
| calcDenovo | 0.001 | 0.000 | 0.001 | |
| calcExp | 3.938 | 0.419 | 4.359 | |
| denovoExpr | 4.512 | 0.432 | 5.259 | |
| denovoGeneExpr-class | 0.001 | 0.001 | 0.002 | |
| denovoGenomeExpr-class | 0.001 | 0.000 | 0.001 | |
| distrsGSE37704 | 0.187 | 0.007 | 0.517 | |
| genePlot | 0.618 | 0.003 | 1.380 | |
| getDistrs | 0.539 | 0.019 | 0.914 | |
| getIsland | 0.108 | 0.002 | 0.110 | |
| getNreads | 0.000 | 0.000 | 0.001 | |
| getReads | 0.001 | 0.000 | 0.000 | |
| getRoc | 0.001 | 0.000 | 0.001 | |
| hg19DB | 0.113 | 0.002 | 0.116 | |
| mergeBatches | 0.148 | 0.001 | 0.148 | |
| mergeExp | 0.001 | 0.000 | 0.000 | |
| modelPrior | 0.612 | 0.007 | 0.636 | |
| modelPriorAS-class | 0.001 | 0.001 | 0.001 | |
| pathCounts-class | 0.001 | 0.000 | 0.001 | |
| pathCounts | 0.001 | 0.000 | 0.001 | |
| plot-methods | 0.001 | 0.000 | 0.000 | |
| plotExpr | 0.001 | 0.000 | 0.000 | |
| plotPriorAS | 0 | 0 | 0 | |
| probNonEquiv | 0.189 | 0.002 | 0.203 | |
| procBam-class | 0.001 | 0.001 | 0.002 | |
| procBam | 0.001 | 0.000 | 0.001 | |
| procGenome | 0.001 | 0.000 | 0.001 | |
| qqnormGenomeWide | 0.075 | 0.001 | 0.077 | |
| quantileNorm | 0.015 | 0.001 | 0.018 | |
| relexprByGene | 0.000 | 0.001 | 0.001 | |
| rmShortInserts | 0.001 | 0.000 | 0.001 | |
| simMAE | 0.001 | 0.000 | 0.001 | |
| simMAEcheck | 0.001 | 0.000 | 0.001 | |
| simMultSamples | 0.001 | 0.000 | 0.001 | |
| simReads | 0.630 | 0.012 | 0.642 | |
| simulatedSamples-class | 0.002 | 0.000 | 0.002 | |
| splitGenomeByLength | 0.000 | 0.001 | 0.001 | |
| transcripts | 0.324 | 0.001 | 0.326 | |
| wrapDenovo | 0.001 | 0.000 | 0.001 | |
| wrapKnown | 0.001 | 0.000 | 0.001 | |