BioC 3.2: CHECK report for LowMACA on zin1

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

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

* 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)

name	user	system	elapsed
LowMACA-class	8.955	1.172	46.639
LowMACA-package	8.129	1.181	31.561
alignSequences	1.904	0.162	13.950
bpAll	2.737	0.235	1.477
entropy	0.915	0.120	1.050
getMutations	0.636	0.074	9.073
lfm	0.730	0.020	0.749
lmAlignment	0.048	0.004	0.052
lmEntropy	1.425	0.227	1.086
lmMutations	0.036	0.000	0.036
lmObj	0.075	0.004	0.079
lmParams	0.559	0.071	0.627
lmPlot	5.807	1.236	5.924
mapMutations	0.537	0.004	0.541
newLowMACA	3.373	0.032	3.408
nullProfile	1.543	0.134	1.101
parallelize	0.609	0.004	0.613
protter	1.496	0.165	7.717
setup	3.612	0.301	56.627
showTumorType	0.025	0.035	0.428