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CHECK report for psichomics on merida2

This page was generated on 2018-10-17 08:57:18 -0400 (Wed, 17 Oct 2018).

Package 1145/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.6.2
Nuno Saraiva-Agostinho
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/psichomics
Branch: RELEASE_3_7
Last Commit: 670cb8a
Last Changed Date: 2018-10-02 05:35:55 -0400 (Tue, 02 Oct 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: psichomics
Version: 1.6.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psichomics_1.6.2.tar.gz
StartedAt: 2018-10-16 23:23:27 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:29:59 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 392.4 seconds
RetCode: 0
Status:  OK 
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psichomics_1.6.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/psichomics.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.6.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘psichomics’ 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 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/psichomics/libs/psichomics.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL psichomics
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘psichomics’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o psichomics.so RcppExports.o psiFastCalc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/psichomics/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’
* DONE (psichomics)

Tests output

psichomics.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(psichomics)
Loading required package: shiny
Loading required package: shinyBS
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
Start the visual interface by running the function psichomics()

Attaching package: 'psichomics'

The following object is masked from 'package:base':

    rowMeans

> 
> test_check("psichomics")
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LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d260d68c3a/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d22b5b3d7/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d211970f90/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d214bb7a75/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d227ec50d/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d28076c6b/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d271b0e177/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d25863df61/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d257de42e7/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d25dfb268/index.html.

Retrieving protein annotation from UniProt...

Plotting protein domains...
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d253444db5/index.html.

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving MISO annotation...

Parsing MISO annotation...
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LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d2246930cd/index.html.

Retrieving SUPPA annotation...

Parsing SUPPA annotation...

Retrieving VAST-TOOLS annotation...

Parsing VAST-TOOLS annotation...

ALT3

ALT5

COMBI

IR

MERGE3m

MIC

EXSK

MULTI
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1090 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 26.731   1.071  38.750 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0020.0000.003
blendColours0.0030.0000.003
correlateGEandAS0.0230.0050.028
createGroupByAttribute0.0030.0000.004
createJunctionsTemplate0.0040.0000.004
diffAnalyses0.1450.0210.166
downloadFiles0.0010.0000.001
ensemblToUniprot0.0870.0100.618
filterGroups0.0020.0000.002
getAttributesTime0.0050.0010.006
getDownloadsFolder0.0010.0000.001
getFirebrowseCohorts1.6370.0041.728
getFirebrowseDataTypes0.0020.0010.002
getFirebrowseDateFormat0.0020.0000.003
getFirebrowseDates0.0140.0010.073
getMatchingSamples0.0030.0000.004
getNumerics0.0050.0000.005
getPatientFromSample0.0030.0010.003
getSplicingEventFromGenes0.0040.0000.004
getSplicingEventTypes0.0010.0000.002
getValidEvents0.0060.0000.007
groupPerElem0.0020.0010.002
hchart.survfit0.3250.0580.397
isFirebrowseUp0.0060.0000.035
labelBasedOnCutoff0.0020.0010.002
leveneTest0.0150.0000.016
listAllAnnotations0.0020.0000.002
listSplicingAnnotations0.0010.0000.002
loadAnnotation0.0010.0000.002
loadFirebrowseData0.0010.0000.001
loadLocalFiles0.0010.0000.001
missingDataModal0.0010.0010.001
normaliseGeneExpression0.0170.0010.018
optimalSurvivalCutoff0.1170.0020.119
parseCategoricalGroups0.0030.0010.004
parseFirebrowseMetadata0.0480.0020.206
parseMatsEvent0.0070.0000.007
parseMatsGeneric0.0360.0020.037
parseMisoAnnotation0.1970.0110.213
parseMisoEvent0.0100.0010.011
parseMisoEventID0.0070.0000.009
parseMisoGeneric0.0630.0030.067
parseMisoId0.0020.0000.002
parseSampleGroups0.0030.0010.004
parseSplicingEvent0.0040.0000.003
parseSuppaEvent0.0050.0010.005
parseSuppaGeneric0.0360.0020.039
parseTcgaSampleInfo0.0050.0000.006
parseUrlsFromFirebrowseResponse0.0200.0010.114
parseVastToolsEvent0.0110.0000.011
parseVastToolsSE0.0390.0020.040
performICA0.0120.0020.015
performPCA0.0030.0000.003
plotCorrelation0.8020.0230.828
plotDistribution0.6770.0630.745
plotGroupIndependence0.2850.0380.323
plotICA0.2160.0260.248
plotPCA0.3080.1200.434
plotProtein0.0020.0000.001
plotSingleICA0.2940.0680.373
plotSurvivalCurves0.1360.0420.197
plotTranscripts0.0210.0010.810
plotVariance0.0760.0250.129
prepareAnnotationFromEvents0.2330.0060.240
prepareFirebrowseArchives0.0030.0000.003
prepareSRAmetadata0.0020.0000.002
processSurvTerms0.0060.0000.006
psichomics0.0010.0000.001
quantifySplicing0.0080.0010.009
queryEnsembl0.0500.0030.527
queryEnsemblByEvent0.1110.0061.336
queryEnsemblByGene0.1100.0061.528
queryFirebrowseData0.0360.0010.234
queryPubMed0.0670.0060.496
queryUniprot0.1990.0060.910
readFile0.0020.0000.002
renameDuplicated0.0030.0000.003
rowMeans0.0020.0000.002
rowVars0.0020.0000.002
sidebar0.0120.0010.013
survdiff.survTerms0.0140.0000.015
survfit.survTerms0.0250.0000.026
testGroupIndependence0.0040.0000.004
testSurvival0.0280.0010.029
textSuggestions0.0020.0000.002
trimWhitespace0.0020.0000.002