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CHECK report for pRoloc on tokay1

This page was generated on 2019-04-13 11:22:31 -0400 (Sat, 13 Apr 2019).

Package 1198/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pRoloc 1.22.2
Laurent Gatto
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/pRoloc
Branch: RELEASE_3_8
Last Commit: 1098398
Last Changed Date: 2019-03-15 18:23:52 -0400 (Fri, 15 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pRoloc
Version: 1.22.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pRoloc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pRoloc_1.22.2.tar.gz
StartedAt: 2019-04-13 04:41:09 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:55:22 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 852.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: pRoloc.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pRoloc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pRoloc_1.22.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pRoloc.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pRoloc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pRoloc' version '1.22.2'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'pRoloc' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-map.Rd:27: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-map.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-map.Rd:79: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-mcmc.Rd:24: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-mcmc.Rd:115: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-mcmc.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pRoloc.Rcheck/00install.out' for details.
* 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
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'MLInterfaces:::.macroF1' 'MLInterfaces:::.precision'
  'MLInterfaces:::.recall' 'MLInterfaces:::es2df'
  'MSnbase:::.sameNbCol' 'MSnbase:::getVariableName'
  'MSnbase:::logging' 'MSnbase:::nologging' 'caret:::predict.plsda'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'pRoloc/R/annotation.R':
  unlockBinding("params", .pRolocEnv)
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/pRoloc/libs/i386/pRoloc.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
perTurboClassification 12.79   0.01   12.81
svmClassification       7.94   0.22    8.15
nnetClassification      7.57   0.02    7.59
SpatProtVis-class       6.72   0.30    7.01
rfClassification        6.78   0.12    6.90
ksvmClassification      5.16   0.04    5.19
ClustDist-class         3.51   0.30    9.60
clustDist               2.64   0.14    6.77
ClustDistList-class     2.39   0.20    6.85
addGoAnnotations        2.31   0.15    6.82
AnnotationParams-class  0.72   0.03    5.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
perTurboClassification 14.97   0.00   15.20
nnetClassification      7.16   0.01    7.17
svmClassification       6.68   0.07    6.74
rfClassification        6.43   0.17    6.59
SpatProtVis-class       5.90   0.30    6.20
ksvmClassification      5.22   0.07    5.30
ClustDist-class         3.56   0.25    7.97
clustDist               2.84   0.15    7.11
addGoAnnotations        2.69   0.05    6.95
ClustDistList-class     2.46   0.06    6.79
AnnotationParams-class  0.72   0.03    6.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/pRoloc.Rcheck/00check.log'
for details.



Installation output

pRoloc.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pRoloc_1.22.2.tar.gz && rm -rf pRoloc.buildbin-libdir && mkdir pRoloc.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pRoloc.buildbin-libdir pRoloc_1.22.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pRoloc_1.22.2.zip && rm pRoloc_1.22.2.tar.gz pRoloc_1.22.2.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 44 2537k   44 1120k    0     0  23.8M      0 --:--:-- --:--:-- --:--:-- 25.4M
100 2537k  100 2537k    0     0  40.7M      0 --:--:-- --:--:-- --:--:-- 42.7M

install for i386

* installing *source* package 'pRoloc' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dmvtCpp.cpp -o dmvtCpp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pRoloc.cpp -o pRoloc.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o pRoloc.dll tmp.def RcppExports.o dmvtCpp.o pRoloc.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/pRoloc.buildbin-libdir/pRoloc/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pRoloc'
    finding HTML links ... done
    AnnotationParams-class                  html  
    ClustDist-class                         html  
    ClustDistList-class                     html  
    GenRegRes-class                         html  
    finding level-2 HTML links ... done

    MCMCParams                              html  
    MLearn-methods                          html  
    MartInstance-class                      html  
    QSep-class                              html  
    SpatProtVis-class                       html  
    addGoAnnotations                        html  
    addLegend                               html  
    addMarkers                              html  
    checkFeatureNamesOverlap                html  
    checkFvarOverlap                        html  
    chi2-methods                            html  
    classWeights                            html  
    clustDist                               html  
    defunct                                 html  
    empPvalues                              html  
    exprsToRatios-methods                   html  
    fDataToUnknown                          html  
    filterBinMSnSet                         html  
    filterMaxMarkers                        html  
    filterMinMarkers                        html  
    filterZeroCols                          html  
    getGOFromFeatures                       html  
    getMarkerClasses                        html  
    getMarkers                              html  
    getNormDist                             html  
    getPredictions                          html  
    getStockcol                             html  
    goIdToTerm                              html  
    highlightOnPlot                         html  
    knnClassification                       html  
    knnOptimisation                         html  
    knntlClassification                     html  
    knntlOptimisation                       html  
    ksvmClassification                      html  
    ksvmOptimisation                        html  
    lopims                                  html  
    makeGoSet                               html  
    markerMSnSet                            html  
    markers                                 html  
    mcmc-helpers                            html  
    minMarkers                              html  
    move2Ds                                 html  
    mrkConsProfiles                         html  
    mrkHClust                               html  
    nbClassification                        html  
    nbOptimisation                          html  
    nndist-methods                          html  
    nnetClassification                      html  
    nnetOptimisation                        html  
    orderGoAnnotations                      html  
    orgQuants                               html  
    pRolocmarkers                           html  
    perTurboClassification                  html  
    perTurboOptimisation                    html  
    phenoDisco                              html  
    plot2D                                  html  
    plot2Ds                                 html  
    plotConsProfiles                        html  
    plotDist                                html  
    plotEllipse                             html  
    plsdaClassification                     html  
    plsdaOptimisation                       html  
    rfClassification                        html  
    rfOptimisation                          html  
    sampleMSnSet                            html  
    showGOEvidenceCodes                     html  
    subsetMarkers                           html  
    svmClassification                       html  
    svmOptimisation                         html  
    tagm-map                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-map.Rd:27: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-map.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-map.Rd:79: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
    tagm-mcmc                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-mcmc.Rd:24: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-mcmc.Rd:115: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAdrchk/R.INSTALL233827b02ce3/pRoloc/man/tagm-mcmc.Rd:90: file link 'MSnSet' in package 'MSnbase' does not exist and so has been treated as a topic
    testMSnSet                              html  
    testMarkers                             html  
    thetas                                  html  
    undocumented                            html  
    zerosInBinMSnSet                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pRoloc' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c dmvtCpp.cpp -o dmvtCpp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pRoloc.cpp -o pRoloc.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o pRoloc.dll tmp.def RcppExports.o dmvtCpp.o pRoloc.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/pRoloc.buildbin-libdir/pRoloc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pRoloc' as pRoloc_1.22.2.zip
* DONE (pRoloc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pRoloc' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

pRoloc.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> 
> # The setting of R_TESTS exists to work around an R bug. See
> # https://github.com/hadley/testthat/issues/144
> # We should remove it when the issue is resolved.
> Sys.setenv("R_TESTS" = "")
> 
> library("testthat")
> library("pRoloc")
Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.8.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws

Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XML

Attaching package: 'annotate'

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

    nChrom

Loading required package: cluster
Loading required package: BiocParallel

This is pRoloc version 1.22.2 
  Visit https://lgatto.github.io/pRoloc/ to get started.

> library("pRolocdata")

This is pRolocdata version 1.20.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRoloc")
Object of class "SpatProtVis"
 Data: dunkley2006 
 Visualisation methods: PCA, MDS, kpca
Done.
Connecting to Biomart...
Object of class "AnnotationParams"
 Using the 'ENSEMBL_MART_ENSEMBL' BioMart database
 Using the 'hsapiens_gene_ensembl' dataset
 Using 'uniprotswissprot' as filter
 Created on Sat Apr 13 04:50:46 2019
Connecting to Biomart...
GO Term Evidence Code
 Experimental Evidence Codes
  EXP: Inferred from Experiment
   IDA: Inferred from Direct Assay
   IPI: Inferred from Physical Interaction
   IMP: Inferred from Mutant Phenotype
   IGI: Inferred from Genetic Interaction
   IEP: Inferred from Expression Pattern
 Computational Analysis Evidence Codes
  ISS: Inferred from Sequence or Structural Similarity
   ISO: Inferred from Sequence Orthology
   ISA: Inferred from Sequence Alignment
   ISM: Inferred from Sequence Model
   IGC: Inferred from Genomic Context
   IBA: Inferred from Biological aspect of Ancestor
   IBD: Inferred from Biological aspect of Descendant
   IKR: Inferred from Key Residues
   IRD: Inferred from Rapid Divergence
   RCA: inferred from Reviewed Computational Analysis
 Author Statement Evidence Codes
   TAS: Traceable Author Statement
   NAS: Non-traceable Author Statement
 Curator Statement Evidence Codes
   IC: Inferred by Curator
   ND: No biological Data available
 Automatically-assigned Evidence Codes
   IEA: Inferred from Electronic Annotation
 Obsolete Evidence Codes
   NR: Not Recorded
Connecting to Biomart...
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5 
   1    3    1    2    3 
organelleMarkers
ORG2 ORG3 ORG5 
   6    1    3 
organelleMarkers
   ORG2 unknown 
      3       7 
organelleMarkers
   ORG2 unknown 
      2       8 
# weights:  269
initial  value 670.632139 
iter  10 value 379.154011
iter  20 value 214.607114
iter  30 value 168.319438
iter  40 value 162.189377
iter  50 value 159.464493
iter  60 value 158.115795
iter  70 value 157.225109
iter  80 value 156.584611
iter  90 value 156.267913
iter 100 value 156.195435
final  value 156.195435 
stopped after 100 iterations
# weights:  269
initial  value 670.632139 
iter  10 value 379.154011
iter  20 value 214.607114
iter  30 value 168.319438
iter  40 value 162.189377
iter  50 value 159.464493
iter  60 value 158.115795
iter  70 value 157.225109
iter  80 value 156.584611
iter  90 value 156.267913
iter 100 value 156.195435
final  value 156.195435 
stopped after 100 iterations
Common markers:  0 
Unique x markers:  49 
Unique y markers:  34 
Common unkowns:  11 
Unique x unknowns:  40 
Unique y unknowns:  66 
               my
mx              ER lumen ER membrane Golgi Mitochondrion  PM Plastid Ribosome
  ER lumen            14           0     0             0   0       0        0
  ER membrane          0          45     0             0   0       0        0
  Golgi                0           0    28             0   0       0        0
  Mitochondrion        0           0     0            55   0       0        0
  PM                   0           0     0             0  46       0        0
  Plastid              0           0     0             0   0      20        0
  Ribosome             0           0     0             0   0       0       19
  TGN                  0           0     0             0   0       0        0
  unknown              0           0     0             0   0       0        0
  vacuole              0           0     0             0   0       0        0
               my
mx              TGN unknown vacuole
  ER lumen        0       0       0
  ER membrane     0       0       0
  Golgi           0       0       0
  Mitochondrion   0       0       0
  PM              0       0       0
  Plastid         0       0       0
  Ribosome        0       0       0
  TGN            13       0       0
  unknown         0     428       0
  vacuole         0       0      21
== testthat results  ===========================================================
OK: 147 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 104.76    3.18  152.01 

pRoloc.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> 
> # The setting of R_TESTS exists to work around an R bug. See
> # https://github.com/hadley/testthat/issues/144
> # We should remove it when the issue is resolved.
> Sys.setenv("R_TESTS" = "")
> 
> library("testthat")
> library("pRoloc")
Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: ProtGenerics

This is MSnbase version 2.8.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws

Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XML

Attaching package: 'annotate'

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

    nChrom

Loading required package: cluster
Loading required package: BiocParallel

This is pRoloc version 1.22.2 
  Visit https://lgatto.github.io/pRoloc/ to get started.

> library("pRolocdata")

This is pRolocdata version 1.20.0.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRoloc")
Object of class "SpatProtVis"
 Data: dunkley2006 
 Visualisation methods: PCA, MDS, kpca
Done.
Connecting to Biomart...
Object of class "AnnotationParams"
 Using the 'ENSEMBL_MART_ENSEMBL' BioMart database
 Using the 'hsapiens_gene_ensembl' dataset
 Using 'uniprotswissprot' as filter
 Created on Sat Apr 13 04:53:21 2019
Connecting to Biomart...
GO Term Evidence Code
 Experimental Evidence Codes
  EXP: Inferred from Experiment
   IDA: Inferred from Direct Assay
   IPI: Inferred from Physical Interaction
   IMP: Inferred from Mutant Phenotype
   IGI: Inferred from Genetic Interaction
   IEP: Inferred from Expression Pattern
 Computational Analysis Evidence Codes
  ISS: Inferred from Sequence or Structural Similarity
   ISO: Inferred from Sequence Orthology
   ISA: Inferred from Sequence Alignment
   ISM: Inferred from Sequence Model
   IGC: Inferred from Genomic Context
   IBA: Inferred from Biological aspect of Ancestor
   IBD: Inferred from Biological aspect of Descendant
   IKR: Inferred from Key Residues
   IRD: Inferred from Rapid Divergence
   RCA: inferred from Reviewed Computational Analysis
 Author Statement Evidence Codes
   TAS: Traceable Author Statement
   NAS: Non-traceable Author Statement
 Curator Statement Evidence Codes
   IC: Inferred by Curator
   ND: No biological Data available
 Automatically-assigned Evidence Codes
   IEA: Inferred from Electronic Annotation
 Obsolete Evidence Codes
   NR: Not Recorded
Connecting to Biomart...
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5 
   1    3    1    2    3 
organelleMarkers
ORG2 ORG3 ORG5 
   6    1    3 
organelleMarkers
   ORG2 unknown 
      3       7 
organelleMarkers
   ORG2 unknown 
      2       8 
# weights:  269
initial  value 670.632139 
iter  10 value 379.154011
iter  20 value 214.607114
iter  30 value 168.319438
iter  40 value 162.189377
iter  50 value 159.464493
iter  60 value 158.115795
iter  70 value 157.225109
iter  80 value 156.584611
iter  90 value 156.267913
iter 100 value 156.195435
final  value 156.195435 
stopped after 100 iterations
# weights:  269
initial  value 670.632139 
iter  10 value 379.154011
iter  20 value 214.607114
iter  30 value 168.319438
iter  40 value 162.189377
iter  50 value 159.464493
iter  60 value 158.115795
iter  70 value 157.225109
iter  80 value 156.584611
iter  90 value 156.267913
iter 100 value 156.195435
final  value 156.195435 
stopped after 100 iterations
Common markers:  0 
Unique x markers:  49 
Unique y markers:  34 
Common unkowns:  11 
Unique x unknowns:  40 
Unique y unknowns:  66 
               my
mx              ER lumen ER membrane Golgi Mitochondrion  PM Plastid Ribosome
  ER lumen            14           0     0             0   0       0        0
  ER membrane          0          45     0             0   0       0        0
  Golgi                0           0    28             0   0       0        0
  Mitochondrion        0           0     0            55   0       0        0
  PM                   0           0     0             0  46       0        0
  Plastid              0           0     0             0   0      20        0
  Ribosome             0           0     0             0   0       0       19
  TGN                  0           0     0             0   0       0        0
  unknown              0           0     0             0   0       0        0
  vacuole              0           0     0             0   0       0        0
               my
mx              TGN unknown vacuole
  ER lumen        0       0       0
  ER membrane     0       0       0
  Golgi           0       0       0
  Mitochondrion   0       0       0
  PM              0       0       0
  Plastid         0       0       0
  Ribosome        0       0       0
  TGN            13       0       0
  unknown         0     428       0
  vacuole         0       0      21
== testthat results  ===========================================================
OK: 147 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 102.06    2.43  141.73 

Example timings

pRoloc.Rcheck/examples_i386/pRoloc-Ex.timings

nameusersystemelapsed
AnnotationParams-class0.720.035.75
ClustDist-class3.510.309.60
ClustDistList-class2.390.206.85
GenRegRes-class0.020.000.01
QSep-class0.950.030.99
SpatProtVis-class6.720.307.01
addGoAnnotations2.310.156.82
addMarkers0.160.000.20
checkFeatureNamesOverlap0.310.020.53
checkFvarOverlap0.020.020.03
chi2-methods000
classWeights0.170.000.17
clustDist2.640.146.77
empPvalues0.110.000.11
exprsToRatios-methods0.150.000.16
fDataToUnknown0.050.000.04
filterBinMSnSet0.140.000.14
filterZeroCols0.090.000.10
getGOFromFeatures0.050.030.19
getMarkerClasses0.030.000.03
getMarkers0.010.020.03
getPredictions0.270.030.30
getStockcol0.090.000.09
goIdToTerm2.030.122.16
highlightOnPlot0.210.020.22
knnClassification1.150.011.17
knntlClassification000
ksvmClassification5.160.045.19
makeGoSet0.470.010.67
markerMSnSet0.250.000.25
markers0.060.000.06
minMarkers0.030.020.05
move2Ds2.020.022.03
mrkConsProfiles0.180.000.18
mrkHClust0.080.000.08
nbClassification2.920.002.92
nndist-methods0.180.030.21
nnetClassification7.570.027.59
orgQuants0.240.000.24
pRolocmarkers0.010.000.62
perTurboClassification12.79 0.0112.81
phenoDisco000
plot2D2.000.152.17
plot2Ds0.370.070.44
plotConsProfiles0.310.010.44
plotDist0.140.020.16
plsdaClassification000
rfClassification6.780.126.90
sampleMSnSet0.060.020.08
showGOEvidenceCodes000
svmClassification7.940.228.15
testMSnSet0.330.020.35
testMarkers0.030.000.03
thetas000
zerosInBinMSnSet2.670.062.80

pRoloc.Rcheck/examples_x64/pRoloc-Ex.timings

nameusersystemelapsed
AnnotationParams-class0.720.036.03
ClustDist-class3.560.257.97
ClustDistList-class2.460.066.79
GenRegRes-class000
QSep-class0.970.020.99
SpatProtVis-class5.90.36.2
addGoAnnotations2.690.056.95
addMarkers0.160.000.16
checkFeatureNamesOverlap0.350.010.36
checkFvarOverlap0.030.000.03
chi2-methods000
classWeights0.110.040.14
clustDist2.840.157.11
empPvalues0.190.000.19
exprsToRatios-methods0.180.020.20
fDataToUnknown0.070.000.07
filterBinMSnSet0.180.000.18
filterZeroCols0.10.00.1
getGOFromFeatures0.010.030.17
getMarkerClasses0.050.000.04
getMarkers0.060.010.08
getPredictions0.450.020.47
getStockcol0.080.000.08
goIdToTerm2.080.142.22
highlightOnPlot0.220.020.23
knnClassification2.240.002.23
knntlClassification000
ksvmClassification5.220.075.30
makeGoSet0.500.000.68
markerMSnSet0.310.000.32
markers0.060.020.08
minMarkers0.060.000.06
move2Ds2.180.062.23
mrkConsProfiles0.260.000.27
mrkHClust0.090.000.09
nbClassification3.050.023.06
nndist-methods0.200.000.21
nnetClassification7.160.017.17
orgQuants0.270.000.26
pRolocmarkers0.010.000.02
perTurboClassification14.97 0.0015.20
phenoDisco000
plot2D2.440.162.75
plot2Ds0.440.020.46
plotConsProfiles0.290.010.31
plotDist0.170.000.17
plsdaClassification000
rfClassification6.430.176.59
sampleMSnSet0.070.000.08
showGOEvidenceCodes000
svmClassification6.680.076.74
testMSnSet0.390.000.39
testMarkers0.030.000.03
thetas0.000.010.01
zerosInBinMSnSet2.620.132.75