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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:customProDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings customProDB_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/customProDB.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'customProDB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'customProDB' version '1.28.0'
* 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 whether package 'customProDB' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
  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
Bed2Range: no visible binding for global variable 'V5'
OutputNovelJun: no visible binding for global variable 'jun_type'
OutputVarproseq: no visible binding for global variable 'genename'
OutputVarproseq: no visible binding for global variable 'txname'
OutputVarproseq: no visible binding for global variable 'proname'
OutputVarproseq: no visible binding for global variable 'aaref'
OutputVarproseq: no visible binding for global variable 'aapos'
OutputVarproseq: no visible binding for global variable 'aavar'
OutputVarproseq: no visible binding for global variable 'rsid'
OutputVarproseq_single: no visible binding for global variable
  'genename'
OutputVarproseq_single: no visible binding for global variable 'txname'
OutputVarproseq_single: no visible binding for global variable
  'proname'
OutputVarproseq_single: no visible binding for global variable 'aaref'
OutputVarproseq_single: no visible binding for global variable 'aapos'
OutputVarproseq_single: no visible binding for global variable 'aavar'
OutputVarproseq_single: no visible binding for global variable 'rsid'
Outputaberrant: no visible binding for global variable 'pro_name'
Positionincoding: no visible binding for global variable 'cds_start'
Positionincoding: no visible binding for global variable 'cds_end'
PrepareAnnotationEnsembl: no visible binding for global variable
  'ensembl_gene_id'
PrepareAnnotationEnsembl: no visible binding for global variable
  'pro_name'
PrepareAnnotationEnsembl: no visible binding for global variable
  'chrom'
PrepareAnnotationEnsembl: no visible binding for global variable 'name'
PrepareAnnotationEnsembl: no visible binding for global variable
  'alleleCount'
PrepareAnnotationEnsembl: no visible binding for global variable
  'alleles'
PrepareAnnotationRefseq: no visible binding for global variable 'name'
PrepareAnnotationRefseq: no visible binding for global variable
  'mrnaAcc'
PrepareAnnotationRefseq: no visible binding for global variable
  'protAcc'
PrepareAnnotationRefseq: no visible binding for global variable
  'transcript'
PrepareAnnotationRefseq: no visible binding for global variable 'chrom'
PrepareAnnotationRefseq: no visible binding for global variable
  'alleleCount'
PrepareAnnotationRefseq: no visible binding for global variable
  'alleles'
PrepareAnnotationRefseq: no visible binding for global variable
  'COSMIC'
Varlocation: no visible binding for global variable 'pro_name'
Undefined global functions or variables:
  COSMIC V5 aapos aaref aavar alleleCount alleles cds_end cds_start
  chrom ensembl_gene_id genename jun_type mrnaAcc name pro_name proname
  protAcc rsid transcript txname
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
PrepareAnnotationEnsembl 15.23   0.45   33.74
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
PrepareAnnotationEnsembl 13.69   0.37   26.43
OutputNovelJun            1.33   0.01   26.33
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/customProDB.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/customProDB_1.28.0.tar.gz && rm -rf customProDB.buildbin-libdir && mkdir customProDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=customProDB.buildbin-libdir customProDB_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL customProDB_1.28.0.zip && rm customProDB_1.28.0.tar.gz customProDB_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  433k  100  433k    0     0  6610k      0 --:--:-- --:--:-- --:--:-- 7342k

install for i386

* installing *source* package 'customProDB' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'customProDB'
    finding HTML links ... done
    Bed2Range                               html  
    InputVcf                                html  
    JunctionType                            html  
    Multiple_VCF                            html  
    OutputNovelJun                          html  
    OutputVarprocodingseq                   html  
    OutputVarproseq                         html  
    OutputVarproseq_single                  html  
    Outputaberrant                          html  
    Outputproseq                            html  
    OutputsharedPro                         html  
    Positionincoding                        html  
    PrepareAnnotationEnsembl                html  
    PrepareAnnotationRefseq                 html  
    SharedJunc                              html  
    Varlocation                             html  
    aaVariation                             html  
    calculateRPKM                           html  
    easyRun                                 html  
    easyRun_mul                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'customProDB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'customProDB' as customProDB_1.28.0.zip
* DONE (customProDB)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'customProDB' successfully unpacked and MD5 sums checked