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CHECK report for spliceSites on merida2

This page was generated on 2019-04-08 12:24:57 -0400 (Mon, 08 Apr 2019).

Package 1541/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spliceSites 1.31.0
Wolfgang Kaisers
Snapshot Date: 2019-04-07 17:01:41 -0400 (Sun, 07 Apr 2019)
URL: https://git.bioconductor.org/packages/spliceSites
Branch: master
Last Commit: 0035a63
Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  ERROR  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: spliceSites
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spliceSites.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spliceSites_1.31.0.tar.gz
StartedAt: 2019-04-08 04:01:56 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 04:04:34 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 157.1 seconds
RetCode: 0
Status:  OK 
CheckDir: spliceSites.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spliceSites.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spliceSites_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/spliceSites.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 ‘spliceSites/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spliceSites’ version ‘1.31.0’
* 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 ‘spliceSites’ can be installed ... 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  as.data.frame.gapSites merge.gapSites
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/spliceSites.Rcheck/00check.log’
for details.



Installation output

spliceSites.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL spliceSites
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘spliceSites’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c spliceSites.c -o spliceSites.o
clang -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 spliceSites.so spliceSites.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/spliceSites/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spliceSites)

Tests output


Example timings

spliceSites.Rcheck/spliceSites-Ex.timings

nameusersystemelapsed
SpliceCountSet-class000
aaGapSites-class0.5990.0050.611
addGeneAligns0.0670.0020.069
addGenomeData-ExpressionSet0.6080.0750.693
addGenomeData-gapSites0.6050.0570.671
addHbond0.1670.0070.173
addMaxEnt0.2070.0050.212
alt_X_ranks0.0160.0000.017
annGapSites-class0.0900.0030.094
annotate-ExpressionSet0.1340.0040.137
annotation0.0220.0010.024
cRanges-class0.0450.0040.049
caRanges-class0.0940.0040.098
cdRanges-class0.8130.1230.944
countByGeneName0.0860.0030.090
dnaGapSites-class0.2920.0080.302
dnaRanges0.3190.0170.341
extractByGeneName0.2160.0030.222
extractRange0.0230.0010.026
gapSites-class0.0380.0020.041
gapSites0.1040.0050.110
getGapSites0.0480.0020.050
hbond-class0.0100.0020.013
keyProfiler-class0.0200.0000.021
lrCodons0.0740.0010.076
maxEnt-class0.0200.0020.022
plotGeneAlignDepth0.0910.0050.099
rangeByGeneName0.0590.0020.062
readCuffGeneFpkm0.0640.0050.072
readExpSet0.0860.0050.092
readMergedBamGaps0.0260.0020.029
readTabledBamGaps0.1540.0070.164
seqlogo0.1530.0170.173
silic_tryp0.0020.0000.002
spliceSites-package0.0460.0040.051
trim0.0290.0020.032
truncateSeq0.0780.0040.082
truncate_seq0.0030.0000.003
trypsinCleave0.0850.0050.091
uniqueJuncAnn0.1130.0030.118
write.files0.0750.0040.080
xCodons0.0290.0030.034
xJunc0.0260.0020.027
xJuncStrand0.0350.0020.036