##############################################################################
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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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/pRoloc.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.30.0’
* 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 ... 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 ... OK
* 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 ... ERROR
Running examples in ‘pRoloc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot2D
> ### Title: Plot organelle assignment data and results.
> ### Aliases: plot2D plot2Dmethods plot3D,MSnSet-method
> 
> ### ** Examples
> 
> library("pRolocdata")

This is pRolocdata version 1.28.0.
Use 'pRolocdata()' to list available data sets.
> data(dunkley2006)
> plot2D(dunkley2006, fcol = NULL)
> plot2D(dunkley2006, fcol = NULL, col = "black")
> plot2D(dunkley2006, fcol = "markers")
> addLegend(dunkley2006,
+           fcol = "markers",
+           where = "topright",
+           cex = 0.5, bty = "n", ncol = 3)
> title(main = "plot2D example")
> ## available methods
> plot2Dmethods
[1] "PCA"    "MDS"    "kpca"   "lda"    "t-SNE"  "nipals" "hexbin" "none"  
[9] "scree" 
> plot2D(dunkley2006, fcol = NULL, method = "kpca", col = "black")
> plot2D(dunkley2006, fcol = NULL, method = "kpca", col = "black",
+        methargs = list(kpar = list(sigma = 1)))
> plot2D(dunkley2006, method = "lda")
> plot2D(dunkley2006, method = "hexbin")
> ## Using transparent colours
> setStockcol(paste0(getStockcol(), "80"))
> plot2D(dunkley2006, fcol = "markers")
> ## New behavious in 1.3.6 when not enough colours
> setStockcol(c("blue", "red", "green"))
> getStockcol() ## only 3 colours to be recycled
[1] "blue"  "red"   "green"
> getMarkers(dunkley2006)
organelleMarkers
     ER lumen   ER membrane         Golgi Mitochondrion            PM 
           14            45            28            55            46 
      Plastid      Ribosome           TGN       unknown       vacuole 
           20            19            13           428            21 
> plot2D(dunkley2006)
Not enough colours: using colours and pch.
> ## reset colours
> setStockcol(NULL)
> plot2D(dunkley2006, method = "none") ## plotting along 2 first fractions
> plot2D(dunkley2006, dims = c(3, 5), method = "none") ## plotting along fractions 3 and 5
> ## pre-calculate PC1 and PC2 coordinates
> pca <- plot2D(dunkley2006, plot=FALSE)
> head(pca)
          PC1 (64.36%) PC2 (22.34%)
AT1G09210    -4.734261   -0.8204175
AT1G21750    -4.615276   -1.1891468
AT1G51760    -4.770573   -1.6292717
AT1G56340    -5.318056   -0.9972462
AT2G32920    -5.135122   -1.5283630
AT2G47470    -4.899410   -0.8145343
> plot2D(pca, method = "none", methargs  = list(dunkley2006))
> 
> ## plotting in 3 dimenstions
> plot3D(dunkley2006)
Loading required package: rgl
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/pRoloc.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pRoloc
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘pRoloc’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c dmvtCpp.cpp -o dmvtCpp.o
In file included from dmvtCpp.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pRoloc.cpp -o pRoloc.o
In file included from pRoloc.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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-darwin18/8.2.0 -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/4.0/Resources/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 version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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 object is masked from 'package:base':

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.16.1 
  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 1.30.0 
  Visit https://lgatto.github.io/pRoloc/ to get started.

> library("pRolocdata")

This is pRolocdata version 1.28.0.
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 Thu May  6 05:04:19 2021
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 2 | SKIP 0 | PASS 146 ]
> 
> proc.time()
   user  system elapsed 
135.087   6.961 182.938