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CHECK report for pRoloc on merida1

This page was generated on 2019-04-16 11:56:38 -0400 (Tue, 16 Apr 2019).

Package 1198/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pRoloc 1.22.2
Laurent Gatto
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 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
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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pRoloc_1.22.2.tar.gz
StartedAt: 2019-04-16 02:01:59 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:11:41 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 581.7 seconds
RetCode: 0
Status:  OK 
CheckDir: pRoloc.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pRoloc_1.22.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/pRoloc.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 ... 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 ‘pRoloc’ 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
perTurboClassification 19.196  0.085  19.357
svmClassification       8.676  0.037   8.740
rfClassification        7.991  0.339   8.369
SpatProtVis-class       6.690  0.160   6.878
ksvmClassification      6.633  0.112   6.769
nnetClassification      6.702  0.020   6.747
ClustDist-class         4.282  0.202  12.464
clustDist               4.015  0.163   9.082
ClustDistList-class     3.281  0.154   8.307
addGoAnnotations        3.013  0.148   7.901
AnnotationParams-class  0.913  0.085   8.015
* 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: 3 NOTEs
See
  ‘/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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pRoloc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘pRoloc’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c dmvtCpp.cpp -o dmvtCpp.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c pRoloc.cpp -o pRoloc.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 pRoloc.so RcppExports.o dmvtCpp.o pRoloc.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pRoloc/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pRoloc)

Tests output

pRoloc.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> 
> # 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
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 Tue Apr 16 02:09:08 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 
139.204   4.618 179.841 

Example timings

pRoloc.Rcheck/pRoloc-Ex.timings

nameusersystemelapsed
AnnotationParams-class0.9130.0858.015
ClustDist-class 4.282 0.20212.464
ClustDistList-class3.2810.1548.307
GenRegRes-class0.0010.0000.002
QSep-class0.9520.0450.999
SpatProtVis-class6.6900.1606.878
addGoAnnotations3.0130.1487.901
addMarkers0.1910.0050.197
checkFeatureNamesOverlap0.4380.0180.456
checkFvarOverlap0.0280.0050.032
chi2-methods0.0070.0000.007
classWeights0.1300.0170.146
clustDist4.0150.1639.082
empPvalues0.2210.0100.232
exprsToRatios-methods0.2190.0230.243
fDataToUnknown0.0440.0050.050
filterBinMSnSet0.2280.0090.238
filterZeroCols0.1190.0170.137
getGOFromFeatures0.0600.0100.353
getMarkerClasses0.0490.0070.058
getMarkers0.0440.0060.050
getPredictions0.3820.0070.396
getStockcol0.1020.0090.112
goIdToTerm2.9880.1303.142
highlightOnPlot0.2560.0070.265
knnClassification1.6310.0201.659
knntlClassification000
ksvmClassification6.6330.1126.769
makeGoSet0.4540.0170.839
markerMSnSet0.2910.0060.298
markers0.0910.0060.101
minMarkers0.0700.0060.077
move2Ds2.5650.0472.622
mrkConsProfiles0.2820.0070.290
mrkHClust0.1080.0040.113
nbClassification4.4920.0244.528
nndist-methods0.2580.0090.271
nnetClassification6.7020.0206.747
orgQuants0.3160.0050.322
pRolocmarkers0.0130.0020.016
perTurboClassification19.196 0.08519.357
phenoDisco0.0000.0000.001
plot2D2.3130.1252.453
plot2Ds0.5530.0530.611
plotConsProfiles0.4660.0100.478
plotDist0.2210.0090.233
plsdaClassification0.0000.0000.001
rfClassification7.9910.3398.369
sampleMSnSet0.1130.0050.120
showGOEvidenceCodes0.0000.0000.001
svmClassification8.6760.0378.740
testMSnSet0.6120.0080.626
testMarkers0.0350.0130.049
thetas0.0100.0040.014
zerosInBinMSnSet2.8750.1343.021