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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SGSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SGSeq_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SGSeq.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 'SGSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SGSeq' version '1.22.0'
* 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 'SGSeq' 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:
  'GenomicRanges:::extraColumnSlotNames'
  'GenomicRanges:::extraColumnSlotsAsDF'
  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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
predictVariantEffects 51.78   0.31   52.09
analyzeFeatures       30.81   0.70   31.53
predictTxFeatures     16.58   0.18   16.75
getSGVariantCounts    10.82   0.12   10.95
getSGFeatureCounts     7.72   0.11    7.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
predictVariantEffects 53.37   0.25   53.62
analyzeFeatures       24.66   0.25   24.91
predictTxFeatures     19.40   0.19   19.58
getSGVariantCounts    10.75   0.22   10.97
getSGFeatureCounts     7.54   0.25    7.78
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/SGSeq.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/SGSeq_1.22.0.tar.gz && rm -rf SGSeq.buildbin-libdir && mkdir SGSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SGSeq.buildbin-libdir SGSeq_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SGSeq_1.22.0.zip && rm SGSeq_1.22.0.tar.gz SGSeq_1.22.0.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 1373k  100 1373k    0     0  10.0M      0 --:--:-- --:--:-- --:--:-- 10.4M

install for i386

* installing *source* package 'SGSeq' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SGSeq'
    finding HTML links ... done
    SGFeatureCounts                         html  
    SGFeatures                              html  
    SGSegments                              html  
    SGVariantCounts                         html  
    SGVariants                              html  
    TxFeatures                              html  
    analyzeFeatures                         html  
    analyzeVariants                         html  
    annotate                                html  
    annotateSGVariants                      html  
    assays                                  html  
    convertToSGFeatures                     html  
    convertToTxFeatures                     html  
    exonCompatible                          html  
    exportFeatures                          html  
    filterFeatures                          html  
    findOverlapsRanges                      html  
    findSGVariants                          html  
    getBamInfo                              html  
    getSGFeatureCounts                      html  
    getSGFeatureCountsPerSample             html  
    getSGVariantCounts                      html  
    gr                                      html  
    importTranscripts                       html  
    junctionCompatible                      html  
    makeSGFeatureCounts                     html  
    makeVariantNames                        html  
    mergeTxFeatures                         html  
    plotCoverage                            html  
    plotFeatures                            html  
    plotSpliceGraph                         html  
    plotVariants                            html  
    predictCandidatesInternal               html  
    predictCandidatesTerminal               html  
    predictExonsInternal                    html  
    predictExonsTerminal                    html  
    predictJunctions                        html  
    predictSpliced                          html  
    predictTxFeatures                       html  
    predictTxFeaturesPerSample              html  
    predictTxFeaturesPerStrand              html  
    predictVariantEffects                   html  
    processTerminalExons                    html  
    removeExonsIsolated                     html  
    sgf_ann                                 html  
    sgf_pred                                html  
    sgfc_ann                                html  
    sgfc_pred                               html  
    sgv_ann                                 html  
    sgv_pred                                html  
    sgvc_ann                                html  
    sgvc_ann_from_bam                       html  
    sgvc_pred                               html  
    sgvc_pred_from_bam                      html  
    si                                      html  
    slots                                   html  
    splicesiteOverlap                       html  
    tx                                      html  
    txf_ann                                 html  
    txf_pred                                html  
    updateObject                            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 'SGSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SGSeq' as SGSeq_1.22.0.zip
* DONE (SGSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SGSeq' successfully unpacked and MD5 sums checked