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This page was generated on 2021-09-13 15:06:22 -0400 (Mon, 13 Sep 2021).

CHECK results for customProDB on tokay2

To the developers/maintainers of the customProDB package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/customProDB.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 426/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
customProDB 1.32.0  (landing page)
Xiaojing Wang
Snapshot Date: 2021-09-12 04:50:10 -0400 (Sun, 12 Sep 2021)
git_url: https://git.bioconductor.org/packages/customProDB
git_branch: RELEASE_3_13
git_last_commit: 6c740d6
git_last_commit_date: 2021-05-19 11:59:12 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: customProDB
Version: 1.32.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:customProDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings customProDB_1.32.0.tar.gz
StartedAt: 2021-09-12 21:09:49 -0400 (Sun, 12 Sep 2021)
EndedAt: 2021-09-12 21:16:44 -0400 (Sun, 12 Sep 2021)
EllapsedTime: 414.6 seconds
RetCode: 0
Status:   OK  
CheckDir: customProDB.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:customProDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings customProDB_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/customProDB.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.32.0'
* 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 15.7   0.34   33.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
PrepareAnnotationEnsembl 13.56   0.19   28.89
* 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-3.13-bioc/meat/customProDB.Rcheck/00check.log'
for details.



Installation output

customProDB.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/customProDB_1.32.0.tar.gz && rm -rf customProDB.buildbin-libdir && mkdir customProDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=customProDB.buildbin-libdir customProDB_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL customProDB_1.32.0.zip && rm customProDB_1.32.0.tar.gz customProDB_1.32.0.zip
###
##############################################################################
##############################################################################


  % 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  438k  100  438k    0     0  1596k      0 --:--:-- --:--:-- --:--:-- 1600k

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_1.32.0.zip
* DONE (customProDB)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'customProDB' successfully unpacked and MD5 sums checked

Tests output


Example timings

customProDB.Rcheck/examples_i386/customProDB-Ex.timings

nameusersystemelapsed
Bed2Range0.080.000.08
InputVcf0.610.441.05
JunctionType0.690.140.83
Multiple_VCF0.690.030.72
OutputNovelJun1.370.081.45
OutputVarprocodingseq0.510.030.54
OutputVarproseq0.530.020.55
OutputVarproseq_single0.530.010.55
Outputaberrant0.320.000.31
Outputproseq0.930.021.06
OutputsharedPro2.650.002.80
Positionincoding0.400.020.42
PrepareAnnotationEnsembl15.70 0.3433.44
PrepareAnnotationRefseq000
SharedJunc0.680.000.67
Varlocation000
aaVariation0.590.000.60
calculateRPKM0.670.000.67
easyRun1.310.011.33
easyRun_mul3.220.043.25

customProDB.Rcheck/examples_x64/customProDB-Ex.timings

nameusersystemelapsed
Bed2Range0.090.000.10
InputVcf1.050.051.10
JunctionType1.80.01.8
Multiple_VCF0.830.050.87
OutputNovelJun1.610.091.71
OutputVarprocodingseq1.030.031.06
OutputVarproseq0.750.020.77
OutputVarproseq_single0.640.010.66
Outputaberrant0.360.020.37
Outputproseq0.780.020.80
OutputsharedPro2.250.032.28
Positionincoding0.430.000.43
PrepareAnnotationEnsembl13.56 0.1928.89
PrepareAnnotationRefseq000
SharedJunc0.590.020.61
Varlocation000
aaVariation0.580.000.57
calculateRPKM0.720.000.72
easyRun1.690.031.72
easyRun_mul4.320.044.38