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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:02:15 -0400 (Wed, 16 Oct 2019).
| Package 213/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| casper 2.18.0 David Rossell
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| 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 |
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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.
casper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL casper ### ############################################################################## ############################################################################## * 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)
casper.Rcheck/casper-Ex.timings
| name | user | system | elapsed | |
| K562.r1l1 | 0.201 | 0.040 | 0.241 | |
| annotatedGenome-class | 0.001 | 0.000 | 0.001 | |
| asymmetryCheck | 0.012 | 0.000 | 0.011 | |
| calcDenovo | 0.001 | 0.000 | 0.000 | |
| calcExp | 3.319 | 0.096 | 3.415 | |
| denovoExpr | 3.408 | 0.124 | 3.620 | |
| denovoGeneExpr-class | 0.001 | 0.000 | 0.000 | |
| denovoGenomeExpr-class | 0 | 0 | 0 | |
| distrsGSE37704 | 0.166 | 0.002 | 0.168 | |
| genePlot | 0.226 | 0.020 | 0.246 | |
| getDistrs | 0.392 | 0.048 | 0.441 | |
| getIsland | 0.082 | 0.000 | 0.083 | |
| getNreads | 0.000 | 0.000 | 0.001 | |
| getReads | 0.001 | 0.000 | 0.000 | |
| getRoc | 0 | 0 | 0 | |
| hg19DB | 0.08 | 0.00 | 0.08 | |
| mergeBatches | 0.077 | 0.000 | 0.078 | |
| mergeExp | 0 | 0 | 0 | |
| modelPrior | 0.307 | 0.004 | 0.326 | |
| modelPriorAS-class | 0.001 | 0.000 | 0.001 | |
| pathCounts-class | 0 | 0 | 0 | |
| pathCounts | 0 | 0 | 0 | |
| plot-methods | 0.001 | 0.000 | 0.000 | |
| plotExpr | 0 | 0 | 0 | |
| plotPriorAS | 0 | 0 | 0 | |
| probNonEquiv | 0.094 | 0.000 | 0.094 | |
| procBam-class | 0 | 0 | 0 | |
| procBam | 0 | 0 | 0 | |
| procGenome | 0 | 0 | 0 | |
| qqnormGenomeWide | 0.055 | 0.000 | 0.055 | |
| quantileNorm | 0.011 | 0.000 | 0.011 | |
| relexprByGene | 0 | 0 | 0 | |
| rmShortInserts | 0 | 0 | 0 | |
| simMAE | 0 | 0 | 0 | |
| simMAEcheck | 0 | 0 | 0 | |
| simMultSamples | 0 | 0 | 0 | |
| simReads | 0.387 | 0.036 | 0.423 | |
| simulatedSamples-class | 0 | 0 | 0 | |
| splitGenomeByLength | 0 | 0 | 0 | |
| transcripts | 0.153 | 0.000 | 0.152 | |
| wrapDenovo | 0 | 0 | 0 | |
| wrapKnown | 0.000 | 0.000 | 0.001 | |