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BioC 3.2: CHECK report for LowMACA on zin1

This page was generated on 2015-08-24 10:50:30 -0700 (Mon, 24 Aug 2015).

Package 554/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LowMACA 1.1.0
Stefano de Pretis , Giorgio Melloni
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LowMACA
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: LowMACA
Version: 1.1.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings LowMACA_1.1.0.tar.gz
StartedAt: 2015-08-24 01:11:57 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 01:18:13 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 376.2 seconds
RetCode: 0
Status:  OK 
CheckDir: LowMACA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings LowMACA_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/LowMACA.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 ‘LowMACA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LowMACA’ version ‘1.1.0’
* 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 ‘LowMACA’ can be installed ... [16s/23s] 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 ... [56s/191s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
LowMACA-class   8.955  1.172  46.639
LowMACA-package 8.129  1.181  31.561
lmPlot          5.807  1.236   5.924
setup           3.612  0.301  56.627
alignSequences  1.904  0.162  13.950
protter         1.496  0.165   7.717
getMutations    0.636  0.074   9.073
* 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: OK

LowMACA.Rcheck/00install.out:

* installing *source* package ‘LowMACA’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: sapply
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: sapply
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
* DONE (LowMACA)

LowMACA.Rcheck/LowMACA-Ex.timings:

nameusersystemelapsed
LowMACA-class 8.955 1.17246.639
LowMACA-package 8.129 1.18131.561
alignSequences 1.904 0.16213.950
bpAll2.7370.2351.477
entropy0.9150.1201.050
getMutations0.6360.0749.073
lfm0.7300.0200.749
lmAlignment0.0480.0040.052
lmEntropy1.4250.2271.086
lmMutations0.0360.0000.036
lmObj0.0750.0040.079
lmParams0.5590.0710.627
lmPlot5.8071.2365.924
mapMutations0.5370.0040.541
newLowMACA3.3730.0323.408
nullProfile1.5430.1341.101
parallelize0.6090.0040.613
protter1.4960.1657.717
setup 3.612 0.30156.627
showTumorType0.0250.0350.428