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BioC 3.6: CHECK report for BatchQC on malbec1

This page was generated on 2017-08-16 13:24:26 -0400 (Wed, 16 Aug 2017).

Package 89/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 1.5.0
Solaiappan Manimaran
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BatchQC
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BatchQC
Version: 1.5.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.5.0.tar.gz
StartedAt: 2017-08-15 21:23:32 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:25:59 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 146.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BatchQC.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BatchQC_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.5.0’
* 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 4.392  0.156   5.829
* 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-3.6-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
batchQC4.3920.1565.829
batchQC_analyze0.3000.0240.328
batchQC_condition_adjusted0.0440.0120.060
batchQC_filter_genes0.0920.0040.096
batchQC_fsva_adjusted0.4120.0000.410
batchQC_num.sv0.1000.0000.102
batchQC_shapeVariation0.2800.0040.286
batchQC_sva0.1960.0000.199
batchQC_svregress_adjusted0.2000.0080.210
batchqc_circosplot0.2920.0000.288
batchqc_correlation0.1440.0000.144
batchqc_corscatter0.0480.0000.048
batchqc_explained_variation0.0280.0040.033
batchqc_heatmap0.1200.0000.121
batchqc_pc_explained_variation0.0560.0000.055
batchqc_pca0.0240.0000.023
batchqc_pca_svd0.1360.0000.134
batchtest0.0600.0000.061
combatPlot0.2040.0000.203
getShinyInput0.0400.0200.059
getShinyInputCombat000
getShinyInputOrig0.0320.0120.048
getShinyInputSVA000
getShinyInputSVAf0.0000.0000.001
getShinyInputSVAr0.0040.0000.000
gnormalize0.0000.0000.001
log2CPM0.0400.0040.042
rnaseq_sim0.1240.0160.141
setShinyInput000
setShinyInputCombat0.0040.0000.000
setShinyInputOrig0.0000.0000.001
setShinyInputSVA0.0000.0000.001
setShinyInputSVAf0.0000.0000.001
setShinyInputSVAr000