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This page was generated on 2022-04-13 12:05:47 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings pRoloc_1.34.0.tar.gz
StartedAt: 2022-04-12 08:49:36 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 09:01:17 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 700.7 seconds
RetCode: 0
Status:   OK  
CheckDir: pRoloc.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings pRoloc_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/pRoloc.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.34.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pRoloc’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.0Mb
* 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
':::' 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
perTurboClassification 10.198  0.108  10.306
SpatProtVis-class       7.749  0.168   7.918
ClustDist-class         6.628  0.503  11.926
clustDist               6.233  0.360  11.071
plot2D                  5.471  0.180   5.419
rfClassification        5.584  0.024   5.607
ClustDistList-class     5.053  0.216   9.470
addGoAnnotations        4.904  0.300   9.401
AnnotationParams-class  2.749  0.153  71.291
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/pRoloc.Rcheck/00check.log’
for details.



Installation output

pRoloc.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL pRoloc
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘pRoloc’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c dmvtCpp.cpp -o dmvtCpp.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pRoloc.cpp -o pRoloc.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o pRoloc.so RcppExports.o dmvtCpp.o pRoloc.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-pRoloc/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pRoloc)

Tests output

pRoloc.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> 
> # 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
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 Tue Apr 12 08:58:31 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 
 98.363   3.346 302.593 

Example timings

pRoloc.Rcheck/pRoloc-Ex.timings

nameusersystemelapsed
AnnotationParams-class 2.749 0.15371.291
ClustDist-class 6.628 0.50311.926
ClustDistList-class5.0530.2169.470
GenRegRes-class0.0010.0000.001
QSep-class1.2350.2161.450
SpatProtVis-class7.7490.1687.918
addGoAnnotations4.9040.3009.401
addMarkers0.1720.0160.188
checkFeatureNamesOverlap0.3320.0280.361
checkFvarOverlap0.0310.0000.031
chi2-methods0.0030.0000.003
classWeights0.1170.0040.121
clustDist 6.233 0.36011.071
empPvalues0.0520.0040.056
fDataToUnknown0.0450.0040.049
filterBinMSnSet0.1450.0080.153
filterZeroCols0.1040.0120.115
getGOFromFeatures0.5750.0160.591
getMarkerClasses0.0370.0000.036
getMarkers0.0250.0120.036
getPredictions0.2240.0200.243
getStockcol0.0910.0040.094
goIdToTerm1.8760.0241.900
highlightOnPlot0.3430.0070.351
knnClassification0.9990.0201.019
knntlClassification000
ksvmClassification3.8230.0403.863
makeGoSet0.7960.0160.812
markerMSnSet0.2110.0200.231
markers0.0540.0120.066
minMarkers0.0500.0020.051
mixing_posterior_check000
move2Ds2.2730.0642.338
mrkConsProfiles0.1770.0040.181
mrkHClust0.0640.0000.063
nbClassification2.0280.0282.056
nicheMeans2D0.0010.0000.000
nndist-methods0.1620.0040.166
nnetClassification4.5990.0364.635
orgQuants0.1720.0040.175
pRolocmarkers0.0090.0000.010
perTurboClassification10.198 0.10810.306
phenoDisco000
plot2D5.4710.1805.419
plot2Ds0.3750.0080.384
plotConsProfiles0.2220.0040.226
plotDist0.1270.0080.136
plsdaClassification000
rfClassification5.5840.0245.607
sampleMSnSet0.0500.0040.054
showGOEvidenceCodes0.0010.0000.001
spatial2D0.0010.0000.000
svmClassification4.7750.0484.822
testMSnSet0.2380.0040.242
testMarkers0.0270.0000.027
thetas0.0070.0000.006
zerosInBinMSnSet2.5930.1602.753