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BioC 3.2: CHECK report for SGSeq on linux1.bioconductor.org

This page was generated on 2015-10-27 17:26:49 -0400 (Tue, 27 Oct 2015).

Package 964/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SGSeq 1.4.0
Leonard Goldstein
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SGSeq
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SGSeq
Version: 1.4.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SGSeq_1.4.0.tar.gz
StartedAt: 2015-10-27 08:04:21 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 08:10:05 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 343.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SGSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SGSeq_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SGSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SGSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SGSeq’ version ‘1.4.0’
* 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 ‘SGSeq’ can be installed ... [17s/17s] 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘GenomicRanges:::extraColumnSlotsAsDF’
  See the note in ?`:::` about the use of this operator.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/65s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
predictVariantEffects 14.888  0.020  14.914
analyzeFeatures       12.772  0.143  12.923
predictTxFeatures      8.467  0.072   8.544
getSGVariantCounts     7.904  0.088   8.003
getSGFeatureCounts     5.327  0.072   5.400
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [92s/92s]
 [92s/92s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/SGSeq.Rcheck/00check.log’
for details.


SGSeq.Rcheck/00install.out:

* installing *source* package ‘SGSeq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SGSeq)

SGSeq.Rcheck/SGSeq-Ex.timings:

nameusersystemelapsed
SGFeatureCounts0.1370.0000.137
SGFeatures0.0240.0000.025
SGVariantCounts0.1720.0000.171
SGVariants0.1360.0000.136
TxFeatures0.0570.0000.057
analyzeFeatures12.772 0.14312.923
analyzeVariants1.5290.0001.530
annotate1.2550.0001.256
assays0.0020.0000.002
convertToSGFeatures1.1420.0001.142
convertToTxFeatures0.2870.0000.287
exportFeatures0.0010.0000.000
findSGVariants0.9810.0000.981
getBamInfo0.6100.0640.675
getSGFeatureCounts5.3270.0725.400
getSGVariantCounts7.9040.0888.003
importTranscripts0.0010.0000.001
makeSGFeatureCounts0.0540.0000.054
makeVariantNames0.0060.0000.006
mergeTxFeatures0.4090.0000.409
plotCoverage0.0010.0000.001
plotFeatures0.0010.0000.001
plotSpliceGraph0.0010.0000.001
plotVariants0.0010.0000.001
predictTxFeatures8.4670.0728.544
predictVariantEffects14.888 0.02014.914
processTerminalExons0.2830.0080.292
slots0.0020.0000.002