##############################################################################
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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:pRoloc.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings pRoloc_1.47.1.tar.gz
###
##############################################################################
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/pRoloc.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘pRoloc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pRoloc’ version ‘1.47.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... INFO
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.3Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getAttributesOfInterest0’ ‘getAttributesOfInterestX’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GenRegRes-class.Rd: MSnSet-class
  MLearn-methods.Rd: MSnSet-class, xvalSpec, MLearn
  QSep-class.Rd: MSnSet-class, Versioned-class
  SpatProtVis-class.Rd: MSnSet-class
  clustDist.Rd: MSnSet-class
  getMarkerClasses.Rd: MSnSet-class
  getMarkers.Rd: MSnSet-class
  getPredictions.Rd: MSnSet-class
  highlightOnPlot.Rd: FeaturesOfInterest-class
  knnClassification.Rd: MSnSet-class, knn
  knnOptimisation.Rd: MSnSet-class, knn
  knntlClassification.Rd: MSnSet-class
  knntlOptimisation.Rd: MSnSet-class
  ksvmClassification.Rd: MSnSet-class, ksvm
  ksvmOptimisation.Rd: MSnSet-class, ksvm
  makeGoSet.Rd: MSnSet-class
  minMarkers.Rd: MSnSet-class
  move2Ds.Rd: MSnSetList
  nbClassification.Rd: MSnSet-class, naiveBayes
  nbOptimisation.Rd: MSnSet-class, naiveBayes
  nnetClassification.Rd: MSnSet-class, nnet
  nnetOptimisation.Rd: MSnSet-class, nnet
  orgQuants.Rd: MSnSet-class
  perTurboClassification.Rd: MSnSet-class, ginv
  perTurboOptimisation.Rd: MSnSet-class, ginv
  phenoDisco.Rd: filterNA
  plot2Ds.Rd: MSnSet-class, MSnSetList
  plsdaClassification.Rd: MSnSet-class, plsda
  plsdaOptimisation.Rd: MSnSet-class, plsda
  rfClassification.Rd: MSnSet-class, randomForest
  rfOptimisation.Rd: MSnSet-class, randomForest
  sampleMSnSet.Rd: MSnSet-class
  svmClassification.Rd: MSnSet-class, svm
  svmOptimisation.Rd: MSnSet-class, svm
  testMSnSet.Rd: MSnSet-class
  testMarkers.Rd: MSnSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 7.450  0.005   7.460
plot2D                 6.818  0.128   6.211
ClustDist-class        2.303  0.063   6.442
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   5.         └─biomaRt:::.listMarts(...)
  ── Error ('test_goannotations.R:9:1'): (code run outside of `test_that()`) ─────
  Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
  Look at ?useEnsembl for details on how to try a mirror site.
  Backtrace:
      ▆
   1. └─pRoloc::setAnnotationParams(inputs = c("Mouse genes", "UniProtKB/Swiss-Prot ID")) at test_goannotations.R:9:1
   2.   └─pRoloc:::getFilterList(m[spidx, "dataset"])
   3.     └─biomaRt::useMart(...)
   4.       └─biomaRt:::.useMart(...)
   5.         └─biomaRt:::.listMarts(...)
  
  [ FAIL 3 | WARN 5 | SKIP 0 | PASS 133 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘v01-pRoloc-tutorial.Rmd’ using rmarkdown
--- finished re-building ‘v01-pRoloc-tutorial.Rmd’

--- re-building ‘v02-pRoloc-ml.Rmd’ using rmarkdown
--- finished re-building ‘v02-pRoloc-ml.Rmd’

--- re-building ‘v03-pRoloc-bayesian.Rmd’ using rmarkdown
--- finished re-building ‘v03-pRoloc-bayesian.Rmd’

--- re-building ‘v04-pRoloc-goannotations.Rmd’ using rmarkdown
--- finished re-building ‘v04-pRoloc-goannotations.Rmd’

--- re-building ‘v05-pRoloc-transfer-learning.Rmd’ using rmarkdown

Quitting from lines 213-247 [hparprep] (v05-pRoloc-transfer-learning.Rmd)
Error: processing vignette 'v05-pRoloc-transfer-learning.Rmd' failed with diagnostics:
Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
--- failed re-building ‘v05-pRoloc-transfer-learning.Rmd’

SUMMARY: processing the following file failed:
  ‘v05-pRoloc-transfer-learning.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/pRoloc.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL pRoloc
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘pRoloc’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c dmvtCpp.cpp -o dmvtCpp.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c pRoloc.cpp -o pRoloc.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o pRoloc.so RcppExports.o dmvtCpp.o pRoloc.o -llapack -L/home/rapidbuild/bbs-3.21-bioc-rapid/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-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)

R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 object is masked from 'package:utils':

    findMatches

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 2.33.2 
  Visit https://lgatto.github.io/MSnbase/ to get started.
 Consider switching to the 'R for Mass Spectrometry'
 packages - see https://RforMassSpectrometry.org for details.


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 1.47.1 
  Visit https://lgatto.github.io/pRoloc/ to get started.

> library("pRolocdata")

This is pRolocdata version 1.45.1.
Use 'pRolocdata()' to list available data sets.
> 
> test_check("pRoloc")
Object of class "SpatProtVis"
 Data: dunkley2006 
 Visualisation methods: PCA, MDS, kpca
Done.
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
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 
[1] "markers"
[1] "xx"
[1] "markers"
[1] "xx"
[1] "markers"
[1] "xx"
[1] "markers"
# 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
[1] "xx"
# 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
[1] "markers"
[1] "xx"
[1] "pd.markers"
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 3 | WARN 5 | SKIP 0 | PASS 133 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_annotation.R:8:5'): AnnotationParams ─────────────────────────
`setAnnotationParams(inputs = c("Human genes", "foo"))` threw an error with unexpected message.
Expected match: "Couldn't find a unique feature type match for 'foo'."
Actual message: "Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.\nLook at ?useEnsembl for details on how to try a mirror site."
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_annotation.R:8:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─pRoloc::setAnnotationParams(inputs = c("Human genes", "foo"))
  7.   └─pRoloc:::getFilterList(m[spidx, "dataset"])
  8.     └─biomaRt::useMart(...)
  9.       └─biomaRt:::.useMart(...)
 10.         └─biomaRt:::.listMarts(...)
── Error ('test_annotation.R:11:5'): AnnotationParams ──────────────────────────
Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
Backtrace:
    ▆
 1. └─pRoloc::setAnnotationParams(inputs = c("Human genes", "UniProtKB/Swiss-Prot ID")) at test_annotation.R:11:5
 2.   └─pRoloc:::getFilterList(m[spidx, "dataset"])
 3.     └─biomaRt::useMart(...)
 4.       └─biomaRt:::.useMart(...)
 5.         └─biomaRt:::.listMarts(...)
── Error ('test_goannotations.R:9:1'): (code run outside of `test_that()`) ─────
Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
Backtrace:
    ▆
 1. └─pRoloc::setAnnotationParams(inputs = c("Mouse genes", "UniProtKB/Swiss-Prot ID")) at test_goannotations.R:9:1
 2.   └─pRoloc:::getFilterList(m[spidx, "dataset"])
 3.     └─biomaRt::useMart(...)
 4.       └─biomaRt:::.useMart(...)
 5.         └─biomaRt:::.listMarts(...)

[ FAIL 3 | WARN 5 | SKIP 0 | PASS 133 ]
Error: Test failures
Execution halted