BioC 3.2: CHECK report for viper on oaxaca

Package: viper

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings viper_1.6.0.tar.gz

StartedAt: 2015-10-27 08:49:06 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:11:31 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 1344.7 seconds

RetCode: 0

Status:  OK

CheckDir: viper.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings viper_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/viper.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.6.0’
* 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 ‘viper’ can be installed ... [3s/3s] OK
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22m/22m] OK
Examples with CPU or elapsed time > 5s
                          user  system elapsed
shadow                 420.109 102.468 524.108
viperSignature-methods 172.553  34.835 207.386
msviperSynergy         106.051  18.045 124.214
msviperCombinatorial    98.027  15.946 114.560
plot.msviper            76.033  14.443  90.677
msviper                 74.577  14.229  88.852
bootstrapViper          64.495   5.624  70.726
bootstrapmsviper         9.690   1.613  11.311
viperRPT                 8.729   1.391  10.120
viper                    8.158   1.350   9.508
ledge                    7.686   0.466   8.153
bootstrapTtest-methods   5.133   0.655   6.670
ttestNull-methods        4.743   0.898   5.643
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/viper.Rcheck/00check.log’
for details.

* installing *source* package ‘viper’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (viper)

name	user	system	elapsed
approxk2d	0.142	0.007	0.150
aracne2regulon	3.325	0.309	3.759
aracne2regulon4cnv	2.887	0.234	3.123
bootstrapTtest-methods	5.133	0.655	6.670
bootstrapViper	64.495	5.624	70.726
bootstrapmsviper	9.690	1.613	11.311
distMode	1.335	0.038	1.374
fcvarna	1.244	0.028	1.272
filterCV-methods	1.434	0.050	1.484
frcv	1.353	0.033	1.391
frvarna	1.368	0.030	1.399
integrateSignatures	2.763	0.408	3.173
ledge	7.686	0.466	8.153
msviper	74.577	14.229	88.852
msviperAnnot	4.332	0.290	4.628
msviperClass	2.989	0.144	3.135
msviperCombinatorial	98.027	15.946	114.560
msviperSynergy	106.051	18.045	124.214
plot.msviper	76.033	14.443	90.677
pruneRegulon	1.413	0.035	1.478
rowTtest-methods	2.711	0.063	2.780
scaleGroups	1.423	0.048	1.474
shadow	420.109	102.468	524.108
signatureDistance	2.804	0.183	2.987
ttestNull-methods	4.743	0.898	5.643
viper	8.158	1.350	9.508
viperRPT	8.729	1.391	10.120
viperSignature-methods	172.553	34.835	207.386