Xiaojing Wang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/customProDB |
| Branch: RELEASE_3_9 |
| Last Commit: 38a8519 |
| Last Changed Date: 2019-05-02 11:53:43 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:28:03 -0400 (Wed, 16 Oct 2019).
| Package 376/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| customProDB 1.24.0 Xiaojing Wang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped |
| Package: customProDB |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:customProDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings customProDB_1.24.0.tar.gz |
| StartedAt: 2019-10-16 03:01:45 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:08:32 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 406.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: customProDB.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:customProDB.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings customProDB_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/customProDB.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.24.0'
* 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 or elapsed time > 5s
user system elapsed
PrepareAnnotationEnsembl 4.11 0.22 14.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
PrepareAnnotationEnsembl 4.92 0.06 17.08
* 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-3.9-bioc/meat/customProDB.Rcheck/00check.log'
for details.
customProDB.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/customProDB_1.24.0.tar.gz && rm -rf customProDB.buildbin-libdir && mkdir customProDB.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=customProDB.buildbin-libdir customProDB_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL customProDB_1.24.0.zip && rm customProDB_1.24.0.tar.gz customProDB_1.24.0.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 8649k 0 --:--:-- --:--:-- --:--:-- 9845k
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_1.24.0.zip
* DONE (customProDB)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'customProDB' successfully unpacked and MD5 sums checked
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customProDB.Rcheck/examples_i386/customProDB-Ex.timings
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customProDB.Rcheck/examples_x64/customProDB-Ex.timings
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