Anh Nhat Tran
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/HPAanalyze |
| Branch: RELEASE_3_12 |
| Last Commit: ae410ad |
| Last Changed Date: 2020-11-24 12:55:41 -0400 (Tue, 24 Nov 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:46 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the HPAanalyze package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 846/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HPAanalyze 1.8.1 (landing page) Anh Nhat Tran
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: HPAanalyze |
| Version: 1.8.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings HPAanalyze_1.8.1.tar.gz |
| StartedAt: 2021-05-06 03:40:41 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:43:37 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 175.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: HPAanalyze.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HPAanalyze.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings HPAanalyze_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/HPAanalyze.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.8.1'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
HPAanalyze/docs/articles/a_HPAanalyze_quick_start_files/elevate-section-attrs-2.0/elevate-section-attrs.js
HPAanalyze/docs/articles/b_HPAanalyze_indepth_files/elevate-section-attrs-2.0/elevate-section-attrs.js
HPAanalyze/docs/articles/c_HPAanalyze_case_query_files/elevate-section-attrs-2.0/elevate-section-attrs.js
HPAanalyze/docs/articles/d_HPAanalyze_case_offline_xml_files/elevate-section-attrs-2.0/elevate-section-attrs.js
HPAanalyze/docs/articles/e_HPAanalyze_case_json_files/elevate-section-attrs-2.0/elevate-section-attrs.js
HPAanalyze/docs/articles/f_HPAanalyze_case_images_files/elevate-section-attrs-2.0/elevate-section-attrs.js
HPAanalyze/docs/articles/z_HPAanalyze_paper_figures_files/elevate-section-attrs-2.0/elevate-section-attrs.js
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'HPAanalyze' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
data 6.5Mb
* 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
hpaListParam: no visible binding for global variable
'hpa_histology_data'
hpaSubset: no visible binding for global variable 'hpa_histology_data'
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'
hpaVis: no visible binding for global variable 'hpa_histology_data'
hpaVisPatho: no visible binding for global variable
'hpa_histology_data'
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
'hpa_histology_data'
hpaVisSubcell: no visible binding for global variable 'gene'
hpaVisSubcell: no visible binding for global variable 'sub_location'
hpaVisSubcell: no visible binding for global variable 'enhanced'
hpaVisSubcell: no visible binding for global variable 'supported'
hpaVisSubcell: no visible binding for global variable 'approved'
hpaVisSubcell: no visible binding for global variable 'uncertain'
hpaVisTissue: no visible binding for global variable
'hpa_histology_data'
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'
Undefined global functions or variables:
age approved cancer cell_line cell_type enhanced gene high
hpa_histology_data imageUrl index intensity level low medium
not_detected patientId patient_count quantity sex staining
sub_location supported tissue tissue_cell uncertain
* 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... ERROR
Running examples in 'HPAanalyze-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hpaXml
> ### Title: Extract details about an individual protein from XML file in one
> ### function
> ### Aliases: hpaXml
>
> ### ** Examples
>
>
> hpaXml(inputXml='ENSG00000131979', extractType=c('ProtClass', 'TissueExprSum', 'Antibody'))
trying URL 'https://www.proteinatlas.org/ENSG00000131979.xml'
Warning in download.file(url = version_to_xml_url(targetEnsemblId, version), :
cannot open URL 'https://www.proteinatlas.org/ENSG00000131979.xml': HTTP status was '503 Service Unavailable'
Error in download.file(url = version_to_xml_url(targetEnsemblId, version), :
cannot open URL 'https://www.proteinatlas.org/ENSG00000131979.xml'
Calls: hpaXml -> hpaXmlGet -> download.file
Execution halted
* 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 ERROR, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/HPAanalyze.Rcheck/00check.log'
for details.
HPAanalyze.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/HPAanalyze_1.8.1.tar.gz && rm -rf HPAanalyze.buildbin-libdir && mkdir HPAanalyze.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HPAanalyze.buildbin-libdir HPAanalyze_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL HPAanalyze_1.8.1.zip && rm HPAanalyze_1.8.1.tar.gz HPAanalyze_1.8.1.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
24 7931k 24 1920k 0 0 56.6M 0 --:--:-- --:--:-- --:--:-- 56.8M
100 7931k 100 7931k 0 0 90.8M 0 --:--:-- --:--:-- --:--:-- 91.1M
install for i386
* installing *source* package 'HPAanalyze' ...
** 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 '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
hpa_histology_data 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 'HPAanalyze' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HPAanalyze' as HPAanalyze_1.8.1.zip
* DONE (HPAanalyze)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'HPAanalyze' successfully unpacked and MD5 sums checked
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HPAanalyze.Rcheck/examples_i386/HPAanalyze-Ex.timings
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HPAanalyze.Rcheck/examples_x64/HPAanalyze-Ex.timings
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