BioC 3.6: CHECK report for LowMACA on malbec1

Package: LowMACA

Version: 1.9.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings LowMACA_1.9.0.tar.gz

StartedAt: 2017-08-16 00:20:55 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:31:03 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 608.5 seconds

RetCode: 0

Status:  OK

CheckDir: LowMACA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings LowMACA_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/LowMACA.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 ‘LowMACA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LowMACA’ version ‘1.9.0’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
allPfamAnalysis      143.000  7.928 150.886
lfmSingleSequence     75.712  4.448  80.469
LowMACA-class         10.808  1.624  38.350
LowMACA-package        8.704  1.584  25.190
setup                  7.808  0.816  67.586
lmPlotSingleSequence   4.532  1.336   6.097
alignSequences         5.048  0.508  17.213
lmPlot                 3.704  1.212   5.148
getMutations           0.720  0.136   7.939
* 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

* installing *source* package ‘LowMACA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
* DONE (LowMACA)

name	user	system	elapsed
BLOSUM62	0.008	0.000	0.010
LowMACA-class	10.808	1.624	38.350
LowMACA-package	8.704	1.584	25.190
LowMACA_AML	0.032	0.012	0.044
alignSequences	5.048	0.508	17.213
allPfamAnalysis	143.000	7.928	150.886
bpAll	1.184	0.000	1.185
entropy	1.352	0.000	1.358
getMutations	0.720	0.136	7.939
lfm	2.148	0.048	2.202
lfmSingleSequence	75.712	4.448	80.469
lmAlignment	0.060	0.008	0.071
lmEntropy	1.172	0.016	1.190
lmMutations	0.036	0.004	0.039
lmObj	0.076	0.004	0.084
lmParams	0.588	0.092	0.698
lmPlot	3.704	1.212	5.148
lmPlotSingleSequence	4.532	1.336	6.097
mapMutations	0.520	0.040	0.562
newLowMACA	2.652	0.188	2.843
nullProfile	1.108	0.032	1.140
parallelize	0.504	0.036	0.540
protter	1.160	0.012	3.615
setup	7.808	0.816	67.586
showTumorType	0.036	0.084	0.345