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This page was generated on 2022-01-26 13:07:08 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for pRoloc on tokay2


To the developers/maintainers of the pRoloc package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pRoloc.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1468/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pRoloc 1.34.0  (landing page)
Laurent Gatto
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/pRoloc
git_branch: RELEASE_3_14
git_last_commit: 5c4ca0d
git_last_commit_date: 2021-10-26 12:05:36 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pRoloc
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pRoloc.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pRoloc_1.34.0.tar.gz
StartedAt: 2022-01-26 00:50:15 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 01:09:17 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 1142.4 seconds
RetCode: 0
Status:   OK  
CheckDir: pRoloc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pRoloc.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pRoloc_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/pRoloc.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.34.0'
* 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 whether package 'pRoloc' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.1Mb
* 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
':::' calls which should be '::':
  'MLInterfaces:::.macroF1' 'MLInterfaces:::.precision'
  'MLInterfaces:::.recall' 'MLInterfaces:::es2df'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: '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 use of PKG_*FLAGS in Makefiles ... 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-3.14-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)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/pRoloc/libs/x64/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 (user + system) or elapsed time > 5s
                        user system elapsed
AnnotationParams-class 15.17   0.08   55.05
perTurboClassification 10.55   0.00   10.57
ClustDist-class         8.69   0.59   12.86
clustDist               8.22   0.24   11.07
addGoAnnotations        7.81   0.17   10.63
ClustDistList-class     7.59   0.20   10.52
nnetClassification      6.61   0.12    6.74
SpatProtVis-class       6.53   0.13    6.65
svmClassification       6.10   0.02    6.11
rfClassification        5.81   0.14    5.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
perTurboClassification 13.05   0.03   13.20
SpatProtVis-class       8.14   0.12    8.26
ClustDist-class         7.70   0.26   10.83
clustDist               7.58   0.23   10.65
nnetClassification      7.27   0.01    7.28
svmClassification       7.11   0.02    7.13
addGoAnnotations        6.78   0.24    9.80
ClustDistList-class     6.56   0.22    9.56
rfClassification        6.21   0.09    6.31
AnnotationParams-class  1.25   0.03   39.16
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/pRoloc.Rcheck/00check.log'
for details.



Installation output

pRoloc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/pRoloc_1.34.0.tar.gz && rm -rf pRoloc.buildbin-libdir && mkdir pRoloc.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pRoloc.buildbin-libdir pRoloc_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL pRoloc_1.34.0.zip && rm pRoloc_1.34.0.tar.gz pRoloc_1.34.0.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
100 2598k  100 2598k    0     0  3214k      0 --:--:-- --:--:-- --:--:-- 3220k

install for i386

* installing *source* package 'pRoloc' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dmvtCpp.cpp -o dmvtCpp.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pRoloc.cpp -o pRoloc.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o pRoloc.dll tmp.def RcppExports.o dmvtCpp.o pRoloc.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/pRoloc.buildbin-libdir/00LOCK-pRoloc/00new/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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/pRoloc.buildbin-libdir/00LOCK-pRoloc/00new/pRoloc/help/qsep.html
    SpatProtVis-class                       html  
    addGoAnnotations                        html  
    addLegend                               html  
    addMarkers                              html  
    checkFeatureNamesOverlap                html  
    checkFvarOverlap                        html  
    chi2-methods                            html  
    classWeights                            html  
    clustDist                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/pRoloc.buildbin-libdir/00LOCK-pRoloc/00new/pRoloc/help/clustDist.html
    defunct                                 html  
    empPvalues                              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  
    makeGoSet                               html  
    markerMSnSet                            html  
    markers                                 html  
    mcmc-helpers                            html  
    minMarkers                              html  
    mixing_posterior_check                  html  
    move2Ds                                 html  
    mrkConsProfiles                         html  
    mrkHClust                               html  
    nbClassification                        html  
    nbOptimisation                          html  
    nicheMeans2D                            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  
    spatial2D                               html  
    subsetMarkers                           html  
    svmClassification                       html  
    svmOptimisation                         html  
    tagm-map                                html  
    tagm-mcmc                               html  
    testMSnSet                              html  
    testMarkers                             html  
    thetas                                  html  
    undocumented                            html  
    zerosInBinMSnSet                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'pRoloc' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dmvtCpp.cpp -o dmvtCpp.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pRoloc.cpp -o pRoloc.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o pRoloc.dll tmp.def RcppExports.o dmvtCpp.o pRoloc.o -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/pRoloc.buildbin-libdir/pRoloc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pRoloc' as pRoloc_1.34.0.zip
* DONE (pRoloc)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'pRoloc' successfully unpacked and MD5 sums checked

Tests output

pRoloc.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.20.4 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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 1.34.0 
  Visit https://lgatto.github.io/pRoloc/ to get started.

> library("pRolocdata")

This is pRolocdata version 1.32.0.
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 Wed Jan 26 01:02:52 2022
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 
   3    2    3    1    1 
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5 
   5    2    1    1    1 
organelleMarkers
   ORG1 unknown 
      3       7 
organelleMarkers
   ORG1 unknown 
      2       8 
# weights:  269
initial  value 666.839513 
iter  10 value 207.573433
iter  20 value 34.513121
iter  30 value 1.438035
iter  40 value 0.496168
iter  50 value 0.419018
iter  60 value 0.386372
iter  70 value 0.360129
iter  80 value 0.324298
iter  90 value 0.294123
iter 100 value 0.252996
final  value 0.252996 
stopped after 100 iterations
# weights:  269
initial  value 666.839513 
iter  10 value 207.573433
iter  20 value 34.513121
iter  30 value 1.438035
iter  40 value 0.496168
iter  50 value 0.419018
iter  60 value 0.386372
iter  70 value 0.360129
iter  80 value 0.324298
iter  90 value 0.294123
iter 100 value 0.252996
final  value 0.252996 
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
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 146 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 146 ]
> 
> proc.time()
   user  system elapsed 
 126.48    4.68  209.12 

pRoloc.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.20.4 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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 1.34.0 
  Visit https://lgatto.github.io/pRoloc/ to get started.

> library("pRolocdata")

This is pRolocdata version 1.32.0.
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 Wed Jan 26 01:06:50 2022
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 
   3    2    3    1    1 
organelleMarkers
ORG1 ORG2 ORG3 ORG4 ORG5 
   5    2    1    1    1 
organelleMarkers
   ORG1 unknown 
      3       7 
organelleMarkers
   ORG1 unknown 
      2       8 
# weights:  269
initial  value 666.839513 
iter  10 value 207.573433
iter  20 value 34.513121
iter  30 value 1.438035
iter  40 value 0.496168
iter  50 value 0.419018
iter  60 value 0.386372
iter  70 value 0.360129
iter  80 value 0.324298
iter  90 value 0.294123
iter 100 value 0.252996
final  value 0.252996 
stopped after 100 iterations
# weights:  269
initial  value 666.839513 
iter  10 value 207.573433
iter  20 value 34.513121
iter  30 value 1.438035
iter  40 value 0.496168
iter  50 value 0.419018
iter  60 value 0.386372
iter  70 value 0.360129
iter  80 value 0.324298
iter  90 value 0.294123
iter 100 value 0.252996
final  value 0.252996 
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
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 146 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 146 ]
> 
> proc.time()
   user  system elapsed 
 123.76    2.28  259.79 

Example timings

pRoloc.Rcheck/examples_i386/pRoloc-Ex.timings

nameusersystemelapsed
AnnotationParams-class15.17 0.0855.05
ClustDist-class 8.69 0.5912.86
ClustDistList-class 7.59 0.2010.52
GenRegRes-class000
QSep-class101
SpatProtVis-class6.530.136.65
addGoAnnotations 7.81 0.1710.63
addMarkers0.240.000.23
checkFeatureNamesOverlap0.530.030.78
checkFvarOverlap0.060.000.07
chi2-methods000
classWeights0.240.030.26
clustDist 8.22 0.2411.07
empPvalues0.090.000.10
fDataToUnknown0.050.000.05
filterBinMSnSet0.140.000.14
filterZeroCols0.100.000.09
getGOFromFeatures0.670.030.80
getMarkerClasses0.030.010.05
getMarkers0.060.000.07
getPredictions0.330.000.33
getStockcol0.130.000.13
goIdToTerm2.030.142.17
highlightOnPlot0.370.030.40
knnClassification1.100.031.13
knntlClassification000
ksvmClassification4.280.104.37
makeGoSet0.680.030.74
markerMSnSet0.220.000.22
markers0.070.000.06
minMarkers0.010.010.03
mixing_posterior_check000
move2Ds2.500.132.62
mrkConsProfiles0.170.030.20
mrkHClust0.060.000.07
nbClassification2.280.032.31
nicheMeans2D000
nndist-methods0.190.050.23
nnetClassification6.610.126.74
orgQuants0.220.020.23
pRolocmarkers000
perTurboClassification10.55 0.0010.57
phenoDisco000
plot2D3.160.143.29
plot2Ds0.370.050.43
plotConsProfiles0.440.030.49
plotDist0.20.00.2
plsdaClassification000
rfClassification5.810.145.95
sampleMSnSet0.060.000.06
showGOEvidenceCodes000
spatial2D000
svmClassification6.100.026.11
testMSnSet0.250.000.25
testMarkers0.030.000.03
thetas000
zerosInBinMSnSet2.690.092.79

pRoloc.Rcheck/examples_x64/pRoloc-Ex.timings

nameusersystemelapsed
AnnotationParams-class 1.25 0.0339.16
ClustDist-class 7.70 0.2610.83
ClustDistList-class6.560.229.56
GenRegRes-class000
QSep-class1.030.051.08
SpatProtVis-class8.140.128.26
addGoAnnotations6.780.249.80
addMarkers0.220.000.22
checkFeatureNamesOverlap0.310.030.34
checkFvarOverlap0.030.000.03
chi2-methods000
classWeights0.130.020.14
clustDist 7.58 0.2310.65
empPvalues0.070.000.07
fDataToUnknown0.040.020.05
filterBinMSnSet0.250.000.25
filterZeroCols0.140.010.15
getGOFromFeatures0.600.050.64
getMarkerClasses0.040.000.05
getMarkers0.070.000.06
getPredictions0.310.000.31
getStockcol0.080.030.11
goIdToTerm1.940.082.02
highlightOnPlot0.390.000.39
knnClassification1.200.041.25
knntlClassification000
ksvmClassification4.920.074.98
makeGoSet0.990.000.98
markerMSnSet0.280.010.30
markers0.060.020.08
minMarkers0.050.000.05
mixing_posterior_check000
move2Ds2.700.062.76
mrkConsProfiles0.210.020.22
mrkHClust0.060.010.08
nbClassification2.480.052.53
nicheMeans2D000
nndist-methods0.190.000.19
nnetClassification7.270.017.28
orgQuants0.230.020.25
pRolocmarkers000
perTurboClassification13.05 0.0313.20
phenoDisco000
plot2D2.560.143.71
plot2Ds0.840.030.87
plotConsProfiles0.340.020.36
plotDist0.210.000.20
plsdaClassification000
rfClassification6.210.096.31
sampleMSnSet0.070.000.06
showGOEvidenceCodes000
spatial2D000
svmClassification7.110.027.13
testMSnSet0.340.010.36
testMarkers0.030.020.04
thetas000
zerosInBinMSnSet2.920.093.02