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BioC 3.4: CHECK report for SGSeq on morelia

This page was generated on 2017-04-15 16:26:00 -0400 (Sat, 15 Apr 2017).

Package 1134/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SGSeq 1.8.1
Leonard Goldstein
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/SGSeq
Last Changed Rev: 124760 / Revision: 128728
Last Changed Date: 2016-12-02 21:05:54 -0500 (Fri, 02 Dec 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SGSeq
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.8.1.tar.gz
StartedAt: 2017-04-15 08:02:53 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 08:11:16 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 502.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SGSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SGSeq_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SGSeq.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.1’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
predictVariantEffects 32.291  0.079  32.588
analyzeFeatures       20.800  0.305  21.119
predictTxFeatures     12.898  0.122  13.033
getSGVariantCounts     7.510  0.115   7.633
getSGFeatureCounts     6.386  0.130   6.524
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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
  ‘/Users/biocbuild/bbs-3.4-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
SGFeatureCounts0.1840.0180.201
SGFeatures0.0380.0060.044
SGVariantCounts0.2680.0010.271
SGVariants0.1800.0000.181
TxFeatures0.0580.0000.058
analyzeFeatures20.800 0.30521.119
analyzeVariants2.1720.0072.202
annotate2.5500.0042.559
assays0.0070.0000.008
convertToSGFeatures1.6540.0021.658
convertToTxFeatures0.4970.0010.498
exportFeatures0.0000.0000.001
findSGVariants1.8440.0031.851
getBamInfo1.3510.1741.540
getSGFeatureCounts6.3860.1306.524
getSGVariantCounts7.5100.1157.633
importTranscripts0.0000.0000.001
makeSGFeatureCounts0.0520.0000.052
makeVariantNames0.0050.0010.006
mergeTxFeatures0.2890.0000.289
plotCoverage0.0010.0000.000
plotFeatures0.0010.0000.000
plotSpliceGraph0.0010.0000.001
plotVariants0.0000.0000.001
predictTxFeatures12.898 0.12213.033
predictVariantEffects32.291 0.07932.588
processTerminalExons0.5090.0010.512
slots0.0050.0000.006