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BioC 3.2: CHECK report for TarSeqQC on zin1

This page was generated on 2016-04-23 10:15:01 -0700 (Sat, 23 Apr 2016).

Package 1044/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TarSeqQC 1.0.3
Gabriela Merino
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/TarSeqQC
Last Changed Rev: 115382 / Revision: 116712
Last Changed Date: 2016-03-29 14:37:20 -0700 (Tue, 29 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TarSeqQC
Version: 1.0.3
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.0.3.tar.gz
StartedAt: 2016-04-23 06:01:02 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:03:26 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 143.6 seconds
RetCode: 0
Status:  OK 
CheckDir: TarSeqQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TarSeqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TarSeqQC’ version ‘1.0.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TarSeqQC’ can be installed ... [9s/10s] 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/12s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
pileupCounts 17.623  1.001   5.975
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [67s/35s]
 [68s/35s] 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/TarSeqQC.Rcheck/00check.log’
for details.


TarSeqQC.Rcheck/00install.out:

* installing *source* package ‘TarSeqQC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘TarSeqQC’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TarSeqQC)

TarSeqQC.Rcheck/TarSeqQC-Ex.timings:

nameusersystemelapsed
TargetExperiment-buildFeaturePanel0.0010.0000.002
TargetExperiment-buildReport0.4230.0030.443
TargetExperiment-constructor0.0020.0000.002
TargetExperiment-getters0.1270.0120.138
TargetExperiment-initialize0.0010.0000.001
TargetExperiment-plot0.0010.0000.001
TargetExperiment-plotAttrExpl0.0010.0000.001
TargetExperiment-plotFeatPerform0.0010.0000.001
TargetExperiment-plotFeature0.0010.0000.001
TargetExperiment-plotGeneAttrPerFeat0.0010.0000.001
TargetExperiment-plotNtdPercentage0.0010.0000.001
TargetExperiment-plotRegion0.0010.0000.002
TargetExperiment-print0.0310.0000.031
TargetExperiment-setters0.0040.0000.004
TargetExperiment-show0.0290.0040.033
TargetExperiment-statistics0.020.000.02
TargetExperiment-summarizePanel0.0640.0190.778
pileupCounts17.623 1.001 5.975