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### Running command:
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###   /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_1.47.4.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) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* 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 ‘1.47.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.1Mb
  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 objects imported by ':::' calls:
  ‘MSnbase:::.sameNbCol’ ‘MSnbase:::getVariableName’
  ‘MSnbase:::logging’ ‘MSnbase:::nologging’ ‘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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in getAnnotationParams() : 'getAnnotationParams' is deprecated.
  Warning in showGOEvidenceCodes() : 'showGOEvidenceCodes' is deprecated.
  Warning in getGOEvidenceCodes() : 'getGOEvidenceCodes' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
perTurboClassification 7.276  0.007   7.686
SpatProtVis-class      6.398  0.070   6.577
AnnotationParams-class 0.177  0.035   6.598
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: inferior call failed
Execution halted
* checking package vignettes ... NOTE
Package vignettes without corresponding tangle output:
  ‘v01-pRoloc-tutorial.Rmd’
  ‘v02-pRoloc-ml.Rmd’
  ‘v03-pRoloc-bayesian.Rmd’
  ‘v05-pRoloc-transfer-learning.Rmd’
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX ....Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
.Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
* DONE

Status: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/pRoloc.Rcheck/00check.log’
for details.