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BioC 2.14: CHECK report for spliceSites on zin2

This page was generated on 2014-10-08 08:50:16 -0700 (Wed, 08 Oct 2014).

Package 750/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spliceSites 1.2.0
Wolfgang Kaisers
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/spliceSites
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: spliceSites
Version: 1.2.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.2.0.tar.gz
StartedAt: 2014-10-08 03:00:43 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 03:03:40 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 176.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: spliceSites.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings spliceSites_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/spliceSites.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘rbamtools’ ‘refGenome’ ‘doBy’ ‘Biobase’ ‘Biostrings’ ‘seqLogo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [17s/18s] 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 ... 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 ... WARNING
Codoc mismatches from documentation object 'readCuffGeneFpkm':
readCuffGeneFpkm
  Code: function(cuff, phenoData, summ = "max")
  Docs: function(cuff, phenoData)
  Argument names in code not in docs:
    summ

* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/spliceSites.Rcheck/00check.log’
for details.

spliceSites.Rcheck/00install.out:

* installing *source* package ‘spliceSites’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c spliceSites.c -o spliceSites.o
gcc -std=gnu99 -shared -L/usr/local/lib -o spliceSites.so spliceSites.o -lm -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/spliceSites.Rcheck/spliceSites/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spliceSites)

spliceSites.Rcheck/spliceSites-Ex.timings:

nameusersystemelapsed
SpliceCountSet-class0.0000.0000.002
aaGapSites-class0.2400.0120.265
addGeneAlignPart0.0760.0000.075
addHbond0.4760.0080.507
addMaxEnt0.5160.0000.547
alt_X_ranks0.0200.0000.022
annGapSites-class0.0880.0040.097
annotate-ExpressionSet0.1600.0000.164
annotation0.0480.0000.048
cRanges-class0.0520.0000.053
caRanges-class0.1080.0040.118
cdRanges-class0.6640.0080.704
countByGeneName0.0840.0040.087
dnaGapSites-class0.5040.0040.524
dnaRanges0.2840.0080.291
extractByGeneName0.2400.0040.254
extractRange0.0320.0000.032
gapSites-class0.0600.0000.071
gapSites0.1400.0080.160
getGapSites0.0520.0040.061
hbond-class0.0120.0000.011
keyProfiler-class0.0200.0000.023
lrCodons0.0400.0000.043
maxEnt-class0.0240.0000.023
rangeByGeneName0.0400.0000.039
readCuffGeneFpkm0.0800.0000.081
readExpSet0.1080.0000.107
readMergedBamGaps0.0320.0000.030
readTabledBamGaps0.0680.0000.066
silic_tryp0.0040.0000.002
spliceSites-package0.0720.0040.077
trim0.0360.0040.041
truncateSeq0.0960.0000.099
truncate_seq0.0000.0000.002
trypsinCleave0.1040.0000.106
uniqueJuncAnn0.1320.0000.150
write.files0.0840.0040.090
xCodons0.0360.0000.038
xJunc0.0320.0040.035
xJuncStrand0.0280.0040.033