Nuno Saraiva-Agostinho
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/psichomics |
| Branch: RELEASE_3_6 |
| Last Commit: 630cafd |
| Last Changed Date: 2018-04-04 12:57:52 -0400 (Wed, 04 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:15:34 -0400 (Thu, 12 Apr 2018).
| Package 1084/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| psichomics 1.4.5 Nuno Saraiva-Agostinho
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: psichomics |
| Version: 1.4.5 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings psichomics_1.4.5.tar.gz |
| StartedAt: 2018-04-12 01:59:01 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:02:50 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 229.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: psichomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings psichomics_1.4.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.4.5’
* 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 ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
doc 5.6Mb
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘psichomics/libs/psichomics.so’:
Found ‘putchar’, possibly from ‘putchar’ (C)
Object: ‘psiFastCalc.o’
Found ‘stdout’, possibly from ‘stdout’ (C)
Object: ‘psiFastCalc.o’
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.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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
getFirebrowseCohorts 5.032 0.004 5.101
queryEnsembl 0.036 0.000 10.867
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck/00check.log’
for details.
psichomics.Rcheck/00install.out
* installing *source* package ‘psichomics’ ...
** libs
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c psiFastCalc.cpp -o psiFastCalc.o
psiFastCalc.cpp: In function ‘Rcpp::NumericMatrix psiFastCalc(const NumericMatrix&, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)’:
psiFastCalc.cpp:30:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t col=0; col < mat.ncol(); col++) {
^
psiFastCalc.cpp:31:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t idx=0; idx < incA.length(); idx++) {
^
psiFastCalc.cpp: In function ‘Rcpp::NumericMatrix psiFastCalc2(const NumericMatrix&, const List&, const List&, int)’:
psiFastCalc.cpp:59:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t col=0; col < mat.ncol(); col++) {
^
psiFastCalc.cpp:60:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t idx=0; idx < inc.length(); idx++) {
^
psiFastCalc.cpp:63:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t k=0; k < incIdx.length(); k++)
^
psiFastCalc.cpp:68:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (size_t k=0; k < excIdx.length(); k++)
^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o psiFastCalc.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck/psichomics/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (psichomics)
psichomics.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
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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Retrieving protein annotation from UniProt...
Plotting protein domains...
Retrieving rMATS annotation...
Parsing rMATS annotation...
Retrieving rMATS annotation...
Parsing rMATS annotation...
Retrieving MISO annotation...
Parsing MISO annotation...
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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: 1071 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
11.684 0.108 27.805
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| blendColours | 0.000 | 0.000 | 0.001 | |
| correlateGEandAS | 0.424 | 0.004 | 0.426 | |
| createGroupByAttribute | 0.004 | 0.000 | 0.002 | |
| createJunctionsTemplate | 0.004 | 0.000 | 0.003 | |
| diffAnalyses | 0.228 | 0.004 | 0.236 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.592 | 0.000 | 1.258 | |
| filterGroups | 0 | 0 | 0 | |
| getAttributesTime | 0.000 | 0.000 | 0.002 | |
| getDownloadsFolder | 0.000 | 0.000 | 0.001 | |
| getFirebrowseCohorts | 5.032 | 0.004 | 5.101 | |
| getFirebrowseDataTypes | 0.000 | 0.000 | 0.001 | |
| getFirebrowseDateFormat | 0.000 | 0.000 | 0.002 | |
| getFirebrowseDates | 0.020 | 0.000 | 0.061 | |
| getMatchingSamples | 0.000 | 0.000 | 0.001 | |
| getNumerics | 0.004 | 0.000 | 0.003 | |
| getPatientFromSample | 0.000 | 0.000 | 0.001 | |
| getSplicingEventFromGenes | 0.032 | 0.000 | 0.034 | |
| getSplicingEventTypes | 0 | 0 | 0 | |
| getValidEvents | 0.004 | 0.000 | 0.004 | |
| groupPerElem | 0 | 0 | 0 | |
| hchart.survfit | 0.960 | 0.024 | 1.113 | |
| isFirebrowseUp | 0.008 | 0.000 | 0.026 | |
| labelBasedOnCutoff | 0.02 | 0.00 | 0.02 | |
| leveneTest | 0.012 | 0.000 | 0.011 | |
| listAllAnnotations | 0.000 | 0.000 | 0.001 | |
| listSplicingAnnotations | 0 | 0 | 0 | |
| loadAnnotation | 0 | 0 | 0 | |
| loadFirebrowseData | 0.000 | 0.000 | 0.001 | |
| loadLocalFiles | 0.000 | 0.000 | 0.001 | |
| missingDataModal | 0.004 | 0.000 | 0.001 | |
| normaliseGeneExpression | 0.068 | 0.000 | 0.070 | |
| optimalSurvivalCutoff | 0.228 | 0.000 | 0.228 | |
| parseCategoricalGroups | 0.000 | 0.000 | 0.001 | |
| parseFirebrowseMetadata | 0.072 | 0.004 | 0.196 | |
| parseMatsEvent | 0.004 | 0.000 | 0.005 | |
| parseMatsGeneric | 0.02 | 0.00 | 0.02 | |
| parseMisoAnnotation | 0.384 | 0.004 | 0.387 | |
| parseMisoEvent | 0.012 | 0.000 | 0.010 | |
| parseMisoEventID | 0.000 | 0.004 | 0.006 | |
| parseMisoGeneric | 0.092 | 0.004 | 0.097 | |
| parseMisoId | 0 | 0 | 0 | |
| parseSampleGroups | 0.004 | 0.000 | 0.001 | |
| parseSplicingEvent | 0.000 | 0.000 | 0.002 | |
| parseSuppaEvent | 0.000 | 0.000 | 0.003 | |
| parseSuppaGeneric | 0.016 | 0.000 | 0.018 | |
| parseTcgaSampleInfo | 0.004 | 0.000 | 0.002 | |
| parseUrlsFromFirebrowseResponse | 0.028 | 0.000 | 0.117 | |
| parseVastToolsEvent | 0.008 | 0.000 | 0.007 | |
| parseVastToolsSE | 0.096 | 0.000 | 0.095 | |
| performICA | 0.004 | 0.000 | 0.006 | |
| performPCA | 0.040 | 0.000 | 0.041 | |
| plotCorrelation | 1.564 | 0.000 | 1.566 | |
| plotDistribution | 0.332 | 0.012 | 0.346 | |
| plotGroupIndependence | 0.148 | 0.004 | 0.150 | |
| plotICA | 0.284 | 0.016 | 0.316 | |
| plotPCA | 0.248 | 0.020 | 0.268 | |
| plotProtein | 0 | 0 | 0 | |
| plotSingleICA | 0.236 | 0.000 | 0.233 | |
| plotSurvivalCurves | 0.084 | 0.000 | 0.086 | |
| plotTranscripts | 0.016 | 0.008 | 1.544 | |
| plotVariance | 0.044 | 0.008 | 0.049 | |
| prepareAnnotationFromEvents | 0.292 | 0.000 | 0.293 | |
| prepareFirebrowseArchives | 0.000 | 0.000 | 0.001 | |
| processSurvTerms | 0.000 | 0.000 | 0.003 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.004 | 0.000 | 0.004 | |
| queryEnsembl | 0.036 | 0.000 | 10.867 | |
| queryEnsemblByEvent | 0.064 | 0.008 | 3.050 | |
| queryEnsemblByGene | 0.076 | 0.004 | 4.041 | |
| queryFirebrowseData | 0.092 | 0.000 | 0.247 | |
| queryPubMed | 0.128 | 0.008 | 0.426 | |
| queryUniprot | 0.196 | 0.000 | 1.171 | |
| readFile | 0.000 | 0.000 | 0.002 | |
| renameDuplicated | 0.000 | 0.000 | 0.001 | |
| rowMeans | 0.000 | 0.000 | 0.001 | |
| rowVars | 0 | 0 | 0 | |
| survdiff.survTerms | 0.008 | 0.000 | 0.008 | |
| survfit.survTerms | 0.028 | 0.000 | 0.030 | |
| testGroupIndependence | 0.048 | 0.000 | 0.047 | |
| testSurvival | 0.028 | 0.000 | 0.027 | |
| textSuggestions | 0.004 | 0.000 | 0.001 | |
| trimWhitespace | 0.000 | 0.000 | 0.001 | |