Anh Nhat Tran
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/HPAanalyze |
| Branch: RELEASE_3_8 |
| Last Commit: 2d7785a |
| Last Changed Date: 2018-10-30 11:42:10 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:36 -0400 (Sat, 13 Apr 2019).
| Package 733/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HPAanalyze 1.0.0 Anh Nhat Tran
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: HPAanalyze |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings HPAanalyze_1.0.0.tar.gz |
| StartedAt: 2019-04-13 03:03:58 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:06:52 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 173.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HPAanalyze.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings HPAanalyze_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/HPAanalyze.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HPAanalyze/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HPAanalyze' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'HPAanalyze' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hpaDownload: no visible binding for global variable 'hpaNormalTissue'
hpaDownload: no visible binding for global variable 'hpaCancer'
hpaDownload: no visible binding for global variable 'Total.patients'
hpaDownload: no visible binding for global variable 'Level'
hpaDownload: no visible binding for global variable 'Count.patients'
hpaDownload: no visible binding for global variable 'hpaSubcellularLoc'
hpaDownload: no visible binding for global variable 'rnaGeneTissue'
hpaDownload: no visible binding for global variable 'rnaGeneCellLine'
hpaSubset: no visible binding for global variable 'gene'
hpaSubset: no visible binding for global variable 'tissue'
hpaSubset: no visible binding for global variable 'cell_type'
hpaSubset: no visible binding for global variable 'cancer'
hpaSubset: no visible binding for global variable 'cell_line'
hpaVisPatho: no visible binding for global variable 'gene'
hpaVisPatho: no visible binding for global variable 'cancer'
hpaVisPatho: no visible binding for global variable 'high'
hpaVisPatho: no visible binding for global variable 'medium'
hpaVisPatho: no visible binding for global variable 'low'
hpaVisPatho: no visible binding for global variable 'not_detected'
hpaVisPatho: no visible binding for global variable 'patient_count'
hpaVisPatho: no visible binding for global variable 'level'
hpaVisSubcell: no visible binding for global variable 'gene'
hpaVisSubcell: no visible binding for global variable 'go_id'
hpaVisSubcell: no visible binding for global variable 'sub_location'
hpaVisTissue: no visible binding for global variable 'gene'
hpaVisTissue: no visible binding for global variable 'tissue'
hpaVisTissue: no visible binding for global variable 'cell_type'
hpaVisTissue: no visible binding for global variable 'level'
hpaVisTissue: no visible binding for global variable 'tissue_cell'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
'patientId'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
'age'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
'sex'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
'staining'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
'intensity'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
'quantity'
hpaXmlTissueExpr : <anonymous>: no visible binding for global variable
'imageUrl'
hpaXmlTissueExprSum: no visible binding for global variable 'tissue'
hpaXmlTissueExprSum: no visible binding for global variable 'imageUrl'
named_vector_list_to_tibble: no visible binding for global variable
'index'
named_vector_list_to_tibble: no visible binding for global variable
'value'
Undefined global functions or variables:
Count.patients Level Total.patients age cancer cell_line cell_type
gene go_id high hpaCancer hpaNormalTissue hpaSubcellularLoc imageUrl
index intensity level low medium not_detected patientId patient_count
quantity rnaGeneCellLine rnaGeneTissue sex staining sub_location
tissue tissue_cell value
* 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 or elapsed time > 5s
user system elapsed
hpaXmlTissueExpr 5.49 0.09 5.70
hpaExport 1.41 0.17 10.01
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
hpaXmlTissueExpr 5.91 0.05 6.07
* 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-3.8-bioc/meat/HPAanalyze.Rcheck/00check.log'
for details.
HPAanalyze.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/HPAanalyze_1.0.0.tar.gz && rm -rf HPAanalyze.buildbin-libdir && mkdir HPAanalyze.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HPAanalyze.buildbin-libdir HPAanalyze_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL HPAanalyze_1.0.0.zip && rm HPAanalyze_1.0.0.tar.gz HPAanalyze_1.0.0.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
50 1451k 50 736k 0 0 16.0M 0 --:--:-- --:--:-- --:--:-- 17.1M
100 1451k 100 1451k 0 0 26.0M 0 --:--:-- --:--:-- --:--:-- 27.2M
install for i386
* installing *source* package 'HPAanalyze' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HPAanalyze'
finding HTML links ... done
hpaDownload html
hpaExport html
hpaListParam html
hpaVis html
hpaVisPatho html
hpaVisSubcell html
hpaVisTissue html
hpaXml html
hpaXmlAntibody html
hpaXmlGet html
hpaXmlProtClass html
hpaXmlTissueExpr html
hpaXmlTissueExprSum html
hpa_downloaded_histology_v18 html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'HPAanalyze' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HPAanalyze' as HPAanalyze_1.0.0.zip
* DONE (HPAanalyze)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'HPAanalyze' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
HPAanalyze.Rcheck/examples_i386/HPAanalyze-Ex.timings
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HPAanalyze.Rcheck/examples_x64/HPAanalyze-Ex.timings
|