BioC 3.4: CHECK report for PharmacoGx on moscato1

Package: PharmacoGx

Version: 1.3.4

Command: rm -rf PharmacoGx.buildbin-libdir PharmacoGx.Rcheck && mkdir PharmacoGx.buildbin-libdir PharmacoGx.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PharmacoGx.buildbin-libdir PharmacoGx_1.3.4.tar.gz >PharmacoGx.Rcheck\00install.out 2>&1 && cp PharmacoGx.Rcheck\00install.out PharmacoGx-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PharmacoGx.buildbin-libdir --install="check:PharmacoGx-install.out" --force-multiarch --no-vignettes --timings PharmacoGx_1.3.4.tar.gz

StartedAt: 2016-09-20 13:51:56 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:56:28 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 271.7 seconds

RetCode: 0

Status:  OK

CheckDir: PharmacoGx.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf PharmacoGx.buildbin-libdir PharmacoGx.Rcheck && mkdir PharmacoGx.buildbin-libdir PharmacoGx.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PharmacoGx.buildbin-libdir PharmacoGx_1.3.4.tar.gz >PharmacoGx.Rcheck\00install.out 2>&1 && cp PharmacoGx.Rcheck\00install.out PharmacoGx-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=PharmacoGx.buildbin-libdir --install="check:PharmacoGx-install.out" --force-multiarch --no-vignettes --timings PharmacoGx_1.3.4.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/PharmacoGx.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PharmacoGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PharmacoGx' version '1.3.4'
* package encoding: UTF-8
* 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 whether package 'PharmacoGx' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
  Note: found 2251 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 NOTE
See
  'D:/biocbld/bbs-3.4-bioc/meat/PharmacoGx.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'PharmacoGx' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'PharmacoGx' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PharmacoGx' as PharmacoGx_1.3.4.zip
* DONE (PharmacoGx)

name	user	system	elapsed
LogLogisticRegression	1.28	0.00	1.28
PharmacoSet	0.01	0.02	1.06
amcc	1.58	0.00	1.58
availablePSets	0	0	0
cellInfo-set	1.56	0.01	1.57
cellInfo	1.90	0.02	1.92
cellNames-set	1.73	0.01	1.75
cellNames	1.7	0.0	1.7
checkPSetStructure	1.62	0.00	1.62
computeABC	2.2	0.0	2.2
computeAUC	1.5	0.0	1.5
computeAmax	1.32	0.00	1.33
computeICn	2.86	0.00	2.85
computeSlope	0	0	0
connectivityScore	0.05	0.00	0.04
cosinePerm	0.03	0.00	0.04
dateCreated	1.58	0.01	1.59
downloadPSet	0	0	0
downloadPertSig	0	0	0
drugDoseResponseCurve	0	0	0
drugInfo-set	1.59	0.00	1.59
drugInfo	1.66	0.02	1.67
drugNames-set	1.65	0.03	1.68
drugNames	1.65	0.01	1.67
drugPerturbationSig	2.28	0.02	2.30
drugSensitivitySig	1.28	0.00	1.27
fNames	1.78	0.03	1.81
featureInfo-set	1.60	0.02	1.63
featureInfo	1.60	0.01	1.60
gwc	1.59	0.02	1.61
intersectList	0	0	0
intersectPSet	1.81	0.01	1.83
mDataNames	1.73	0.00	1.73
mcc	2.97	0.00	2.97
molecularProfiles-set	1.64	0.02	1.65
molecularProfiles	2.21	0.11	2.32
pSetName	1.67	0.01	1.69
pertNumber-set	1.68	0.02	1.70
pertNumber	1.69	0.01	1.70
phenoInfo-set	1.71	0.02	1.73
phenoInfo	2.06	0.06	2.12
sensNumber-set	1.73	0.00	1.73
sensNumber	1.84	0.03	1.87
sensitivityInfo-set	1.72	0.02	1.73
sensitivityInfo	2.31	0.14	2.45
sensitivityMeasures	1.68	0.05	1.74
sensitivityProfiles-set	1.75	0.03	1.77
sensitivityProfiles	2.18	0.09	2.28
show-PharmacoSet-method	1.69	0.00	1.69
show-PharmacoSig-method	1.24	0.02	1.25
showSigAnnot	1.26	0.00	1.26
subsetTo	1.79	0.01	1.81
summarizeMolecularProfiles	0.15	0.00	0.14
summarizeSensitivityProfiles	0.31	0.00	0.32
unionList	0	0	0

name	user	system	elapsed
LogLogisticRegression	1.81	0.00	1.81
PharmacoSet	0.01	0.03	0.04
amcc	1.72	0.00	1.72
availablePSets	0	0	0
cellInfo-set	1.25	0.00	1.25
cellInfo	1.40	0.05	1.45
cellNames-set	1.34	0.01	1.36
cellNames	1.37	0.02	1.38
checkPSetStructure	1.3	0.0	1.3
computeABC	2.92	0.00	2.92
computeAUC	1.7	0.0	1.7
computeAmax	1.71	0.00	1.71
computeICn	3.5	0.0	3.5
computeSlope	0	0	0
connectivityScore	0.05	0.00	0.05
cosinePerm	0.06	0.00	0.06
dateCreated	1.51	0.01	1.53
downloadPSet	0	0	0
downloadPertSig	0	0	0
drugDoseResponseCurve	0	0	0
drugInfo-set	1.3	0.0	1.3
drugInfo	1.33	0.05	1.37
drugNames-set	1.31	0.05	1.36
drugNames	1.32	0.04	1.37
drugPerturbationSig	2.97	0.00	2.96
drugSensitivitySig	1.34	0.04	1.38
fNames	1.42	0.00	1.42
featureInfo-set	1.35	0.00	1.35
featureInfo	1.39	0.03	1.42
gwc	1.41	0.00	1.41
intersectList	0	0	0
intersectPSet	1.57	0.01	1.59
mDataNames	1.38	0.02	1.39
mcc	3.3	0.0	3.3
molecularProfiles-set	1.31	0.00	1.31
molecularProfiles	1.91	0.11	2.02
pSetName	1.52	0.01	1.54
pertNumber-set	1.42	0.02	1.44
pertNumber	1.30	0.03	1.35
phenoInfo-set	1.65	0.00	1.66
phenoInfo	1.64	0.01	1.66
sensNumber-set	1.29	0.02	1.31
sensNumber	1.41	0.02	1.42
sensitivityInfo-set	1.29	0.00	1.29
sensitivityInfo	1.93	0.11	2.04
sensitivityMeasures	1.34	0.03	1.37
sensitivityProfiles-set	1.28	0.04	1.33
sensitivityProfiles	1.78	0.13	1.90
show-PharmacoSet-method	1.33	0.01	1.34
show-PharmacoSig-method	1.27	0.00	1.59
showSigAnnot	1.49	0.00	1.48
subsetTo	1.43	0.00	1.44
summarizeMolecularProfiles	0.14	0.00	0.14
summarizeSensitivityProfiles	0.3	0.0	0.3
unionList	0.01	0.00	0.01