BioC 3.2: CHECK report for CoverageView on zin1
This page was generated on 2015-08-24 10:49:52 -0700 (Mon, 24 Aug 2015).
CoverageView 1.5.2 Ernesto Lowy
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CoverageView | Last Changed Rev: 106374 / Revision: 107696 | Last Changed Date: 2015-07-14 11:27:36 -0700 (Tue, 14 Jul 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |  |
Summary
Package: CoverageView |
Version: 1.5.2 |
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CoverageView_1.5.2.tar.gz |
StartedAt: 2015-08-23 22:59:12 -0700 (Sun, 23 Aug 2015) |
EndedAt: 2015-08-23 23:01:31 -0700 (Sun, 23 Aug 2015) |
EllapsedTime: 138.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CoverageView.Rcheck |
Warnings: 1 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings CoverageView_1.5.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/CoverageView.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 ‘CoverageView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoverageView’ version ‘1.5.2’
* 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 ‘CoverageView’ can be installed ... [13s/13s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘BiocGenerics::parLapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parApply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterApplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterExport’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parSapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterCall’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterApply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parSapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parCapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parLapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterMap’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterEvalQ’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parRapply’ when loading ‘CoverageView’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/CoverageView.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
cov.bin,ANY-missing-numeric-missing-CoverageBamFile-missing : .local:
no visible global function definition for ‘Rle’
cov.bin,ANY-numeric-missing-missing-CoverageBamFile-missing : .local:
no visible global function definition for ‘Rle’
cov.bin,missing-missing-missing-missing-CoverageBamFile-character :
.local: no visible global function definition for ‘Rle’
cov.interval,CoverageBigWigFile-CoverageBigWigFile: no visible global
function definition for ‘runLength’
* 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 ... [14s/12s] 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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/CoverageView.Rcheck/00check.log’
for details.
CoverageView.Rcheck/00install.out:
* installing *source* package ‘CoverageView’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘BiocGenerics::parLapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parApply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterApplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterExport’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parSapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterCall’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterApply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parSapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parCapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parLapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterMap’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterEvalQ’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parRapply’ when loading ‘CoverageView’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘BiocGenerics::parLapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parApply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterApplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterExport’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parSapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterCall’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterApply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parSapplyLB’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parCapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parLapply’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterMap’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::clusterEvalQ’ when loading ‘CoverageView’
Warning: replacing previous import by ‘BiocGenerics::parRapply’ when loading ‘CoverageView’
* DONE (CoverageView)
CoverageView.Rcheck/CoverageView-Ex.timings:
name | user | system | elapsed
|
CoverageBamFile-class | 0.019 | 0.000 | 0.018 |
|
CoverageBigWigFile-class | 0.003 | 0.004 | 0.008 |
|
cov.interval | 0.483 | 0.020 | 0.504 |
|
cov.matrix | 2.305 | 0.897 | 1.869 |
|
draw.heatmap | 2.218 | 0.060 | 2.277 |
|
draw.profile | 0.160 | 0.004 | 0.164 |
|
export.wig | 0.129 | 0.004 | 0.130 |
|
genome.covplot.cumdepth | 0.389 | 0.004 | 0.394 |
|
genome.covplot.depth | 0.390 | 0.000 | 0.398 |
|
write.profile | 0.205 | 0.100 | 0.210 |
|