BioC 2.13: CHECK report for spliceSites on perceval
This page was generated on 2014-04-05 09:53:16 -0700 (Sat, 05 Apr 2014).
spliceSites 1.0.0 Wolfgang Kaisers
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/spliceSites | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
Summary
Package: spliceSites |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spliceSites_1.0.0.tar.gz |
StartedAt: 2014-04-05 04:34:39 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 04:39:54 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 314.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spliceSites.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/spliceSites.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.0’
* 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 ... [33s/34s] 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 ... OK
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [26s/26s] 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
spliceSites.Rcheck/00install.out:
* installing *source* package ‘spliceSites’ ...
** libs
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 spliceSites.c -o spliceSites.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/spliceSites.Rcheck/spliceSites/libs
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘rbamtools::coerce’ when loading ‘spliceSites’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘rbamtools::coerce’ when loading ‘spliceSites’
* DONE (spliceSites)
spliceSites.Rcheck/spliceSites-Ex.timings:
name | user | system | elapsed
|
SpliceCountSet-class | 0.002 | 0.003 | 0.006 |
|
aaGapSites-class | 0.770 | 0.046 | 0.844 |
|
addGeneAlignPart | 0.122 | 0.008 | 0.137 |
|
addHbond | 0.948 | 0.034 | 1.000 |
|
addMaxEnt | 0.460 | 0.023 | 0.486 |
|
alt_X_ranks | 0.038 | 0.007 | 0.046 |
|
annGapSites-class | 0.138 | 0.016 | 0.153 |
|
annotate-ExpressionSet | 0.250 | 0.016 | 0.268 |
|
annotation | 0.080 | 0.011 | 0.093 |
|
cRanges-class | 0.097 | 0.016 | 0.114 |
|
caRanges-class | 0.180 | 0.014 | 0.196 |
|
cdRanges-class | 1.652 | 0.290 | 1.980 |
|
countByGeneName | 0.132 | 0.015 | 0.156 |
|
dnaGapSites-class | 0.851 | 0.019 | 0.884 |
|
dnaRanges | 0.377 | 0.027 | 0.414 |
|
extractByGeneName | 0.307 | 0.022 | 0.331 |
|
extractRange | 0.052 | 0.009 | 0.064 |
|
gapSites-class | 0.089 | 0.015 | 0.138 |
|
gapSites | 0.240 | 0.022 | 0.262 |
|
getGapSites | 0.086 | 0.011 | 0.096 |
|
hbond-class | 0.015 | 0.007 | 0.021 |
|
keyProfiler-class | 0.042 | 0.012 | 0.053 |
|
lrCodons | 0.062 | 0.014 | 0.076 |
|
maxEnt-class | 0.034 | 0.013 | 0.047 |
|
rangeByGeneName | 0.057 | 0.011 | 0.067 |
|
readCuffGeneFpkm | 0.117 | 0.013 | 0.131 |
|
readExpSet | 0.138 | 0.015 | 0.156 |
|
readMergedBamGaps | 0.041 | 0.009 | 0.050 |
|
readTabledBamGaps | 0.098 | 0.014 | 0.113 |
|
silic_tryp | 0.010 | 0.003 | 0.014 |
|
spliceSites-package | 0.103 | 0.018 | 0.124 |
|
trim | 0.555 | 0.019 | 0.582 |
|
truncateSeq | 0.129 | 0.019 | 0.149 |
|
truncate_seq | 0.005 | 0.004 | 0.009 |
|
trypsinCleave | 0.146 | 0.017 | 0.166 |
|
uniqueJuncAnn | 0.185 | 0.017 | 0.208 |
|
write.files | 0.119 | 0.014 | 0.133 |
|
xCodons | 0.051 | 0.013 | 0.063 |
|
xJunc | 0.056 | 0.010 | 0.066 |
|
xJuncStrand | 0.050 | 0.011 | 0.061 |
|