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BioC 3.5: CHECK report for BatchQC on malbec2

This page was generated on 2017-08-16 13:17:31 -0400 (Wed, 16 Aug 2017).

Package 90/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 1.4.0
Solaiappan Manimaran
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/BatchQC
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BatchQC
Version: 1.4.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.4.0.tar.gz
StartedAt: 2017-08-15 21:20:43 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:23:06 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 142.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BatchQC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/BatchQC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BatchQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BatchQC’ 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 ‘BatchQC’ 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 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 ... NOTE
gls.series.C: no visible global function definition for ‘lm.fit’
Undefined global functions or variables:
  lm.fit
Consider adding
  importFrom("stats", "lm.fit")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘lmFitC’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
batchQC 4.576  0.152   7.859
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/BatchQC.Rcheck/00check.log’
for details.


BatchQC.Rcheck/00install.out:

* installing *source* package ‘BatchQC’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BatchQC)

BatchQC.Rcheck/BatchQC-Ex.timings:

nameusersystemelapsed
batchQC4.5760.1527.859
batchQC_analyze0.1880.0240.212
batchQC_condition_adjusted0.0440.0000.043
batchQC_filter_genes0.0560.0000.055
batchQC_fsva_adjusted0.2520.0000.252
batchQC_num.sv0.0760.0000.075
batchQC_shapeVariation0.1680.0000.169
batchQC_sva0.1880.0000.187
batchQC_svregress_adjusted0.1360.0080.143
batchqc_circosplot0.2000.0000.199
batchqc_correlation0.1440.0000.144
batchqc_corscatter0.0480.0000.049
batchqc_explained_variation0.0320.0000.033
batchqc_heatmap0.1200.0000.118
batchqc_pc_explained_variation0.0480.0000.050
batchqc_pca0.0200.0040.027
batchqc_pca_svd0.1240.0000.125
batchtest0.0560.0000.058
combatPlot0.1160.0000.115
getShinyInput0.0360.0200.056
getShinyInputCombat0.0000.0000.001
getShinyInputOrig0.0280.0200.046
getShinyInputSVA0.0000.0000.001
getShinyInputSVAf0.0000.0000.001
getShinyInputSVAr000
gnormalize000
log2CPM0.0360.0040.040
rnaseq_sim0.1040.0240.127
setShinyInput0.0000.0000.001
setShinyInputCombat000
setShinyInputOrig000
setShinyInputSVA000
setShinyInputSVAf000
setShinyInputSVAr0.0000.0000.001