| Back to Multiple platform build/check report for BioC 3.10 |
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This page was generated on 2020-04-12 12:48:50 -0400 (Sun, 12 Apr 2020).
| Package 1778/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| UniProt.ws 2.26.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | TIMEOUT | OK |
| Package: UniProt.ws |
| Version: 2.26.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UniProt.ws.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings UniProt.ws_2.26.0.tar.gz |
| StartedAt: 2020-04-12 07:18:15 -0400 (Sun, 12 Apr 2020) |
| EndedAt: 2020-04-12 07:24:37 -0400 (Sun, 12 Apr 2020) |
| EllapsedTime: 382.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: UniProt.ws.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UniProt.ws.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings UniProt.ws_2.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/UniProt.ws.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'UniProt.ws/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'UniProt.ws' version '2.26.0'
* 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 'UniProt.ws' 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'UniProt.ws-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UniProt.ws-objects
> ### Title: UniProt.ws objects and their related methods and functions
> ### Aliases: UniProt.ws class:UniProt.ws UniProt.ws-class
> ### show,UniProt.ws-method species species,UniProt.ws-method taxId
> ### taxId,UniProt.ws-method taxId<- taxId<-,UniProt.ws-method cols
> ### columns columns,UniProt.ws-method keytypes keytypes,UniProt.ws-method
> ### keys keys,UniProt.ws-method select select,UniProt.ws-method
> ### availableUniprotSpecies lookupUniprotSpeciesFromTaxId
> ### Keywords: classes methods
>
> ### ** Examples
>
> ## Make a UniProt.ws object
> up <- UniProt.ws(taxId=9606)
Warning in file(con, "r") :
InternetOpenUrl failed: 'The operation timed out'
Error in file(con, "r") : cannot open the connection
Calls: UniProt.ws -> .getUniprots -> readLines -> file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'UniProt.ws-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UniProt.ws-objects
> ### Title: UniProt.ws objects and their related methods and functions
> ### Aliases: UniProt.ws class:UniProt.ws UniProt.ws-class
> ### show,UniProt.ws-method species species,UniProt.ws-method taxId
> ### taxId,UniProt.ws-method taxId<- taxId<-,UniProt.ws-method cols
> ### columns columns,UniProt.ws-method keytypes keytypes,UniProt.ws-method
> ### keys keys,UniProt.ws-method select select,UniProt.ws-method
> ### availableUniprotSpecies lookupUniprotSpeciesFromTaxId
> ### Keywords: classes methods
>
> ### ** Examples
>
> ## Make a UniProt.ws object
> up <- UniProt.ws(taxId=9606)
Warning in file(con, "r") :
InternetOpenUrl failed: 'The operation timed out'
Error in file(con, "r") : cannot open the connection
Calls: UniProt.ws -> .getUniprots -> readLines -> file
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'UniProt.ws_unit_tests.R'
ERROR
Running the tests in 'tests/UniProt.ws_unit_tests.R' failed.
Last 13 lines of output:
FAILURE in test_mapUniprot: Error in checkTrue(dim(res)[1] > 1) : Test not TRUE
Test files with failing tests
test_select.R
C:/Users/biocbuild/bbs-3.10-bioc/R/library/UniProt.ws/unitTests/test_select.R
test_serviceAccessors.R
test_mapUniprot
Error in BiocGenerics:::testPackage("UniProt.ws") :
unit tests failed for package UniProt.ws
Execution halted
** running tests for arch 'x64' ...
Running 'UniProt.ws_unit_tests.R'
ERROR
Running the tests in 'tests/UniProt.ws_unit_tests.R' failed.
Last 13 lines of output:
FAILURE in test_mapUniprot: Error in checkTrue(dim(res)[1] > 1) : Test not TRUE
Test files with failing tests
test_select.R
C:/Users/biocbuild/bbs-3.10-bioc/R/library/UniProt.ws/unitTests/test_select.R
test_serviceAccessors.R
test_mapUniprot
Error in BiocGenerics:::testPackage("UniProt.ws") :
unit tests failed for package UniProt.ws
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: 4 ERRORs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/UniProt.ws.Rcheck/00check.log'
for details.
UniProt.ws.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/UniProt.ws_2.26.0.tar.gz && rm -rf UniProt.ws.buildbin-libdir && mkdir UniProt.ws.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=UniProt.ws.buildbin-libdir UniProt.ws_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL UniProt.ws_2.26.0.zip && rm UniProt.ws_2.26.0.tar.gz UniProt.ws_2.26.0.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 671k 100 671k 0 0 2923k 0 --:--:-- --:--:-- --:--:-- 2971k
install for i386
* installing *source* package 'UniProt.ws' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'UniProt.ws'
finding HTML links ... done
UniProtWS-class html
colsAndKeytypes html
utilities 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 'UniProt.ws' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'UniProt.ws' as UniProt.ws_2.26.0.zip
* DONE (UniProt.ws)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'UniProt.ws' successfully unpacked and MD5 sums checked
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UniProt.ws.Rcheck/tests_i386/UniProt.ws_unit_tests.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("UniProt.ws")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") : InternetOpenUrl failed: 'The operation timed out'
Getting extra data for P04217, P30443
Getting extra data for P13368, P20806, Q9UM73... (5 total)
Getting extra data for P13368, P20806, Q9UM73... (5 total)
Getting mapping data for P13368 ... and P_REFSEQ_AC
error while trying to retrieve data in chunk 1:
no results after 5 attempts; please try again later
continuing to try
Timing stopped at: 0.3 0.31 52.82
Error in checkTrue(dim(res)[1] > 1) : Test not TRUE
RUNIT TEST PROTOCOL -- Sun Apr 12 07:22:51 2020
***********************************************
Number of test functions: 9
Number of errors: 1
Number of failures: 1
1 Test Suite :
UniProt.ws RUnit Tests - 9 test functions, 1 error, 1 failure
ERROR in C:/Users/biocbuild/bbs-3.10-bioc/R/library/UniProt.ws/unitTests/test_select.R: Error while sourcing C:/Users/biocbuild/bbs-3.10-bioc/R/library/UniProt.ws/unitTests/test_select.R : Error in file(con, "r") : cannot open the connection
FAILURE in test_mapUniprot: Error in checkTrue(dim(res)[1] > 1) : Test not TRUE
Test files with failing tests
test_select.R
C:/Users/biocbuild/bbs-3.10-bioc/R/library/UniProt.ws/unitTests/test_select.R
test_serviceAccessors.R
test_mapUniprot
Error in BiocGenerics:::testPackage("UniProt.ws") :
unit tests failed for package UniProt.ws
Execution halted
|
UniProt.ws.Rcheck/tests_x64/UniProt.ws_unit_tests.Rout.fail
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("UniProt.ws")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") : InternetOpenUrl failed: 'The operation timed out'
Getting extra data for P04217, P30443
Getting extra data for P13368, P20806, Q9UM73... (5 total)
Getting extra data for P13368, P20806, Q9UM73... (5 total)
Getting mapping data for P13368 ... and P_REFSEQ_AC
error while trying to retrieve data in chunk 1:
no results after 5 attempts; please try again later
continuing to try
Timing stopped at: 0.58 0.19 52.46
Error in checkTrue(dim(res)[1] > 1) : Test not TRUE
RUNIT TEST PROTOCOL -- Sun Apr 12 07:24:30 2020
***********************************************
Number of test functions: 9
Number of errors: 1
Number of failures: 1
1 Test Suite :
UniProt.ws RUnit Tests - 9 test functions, 1 error, 1 failure
ERROR in C:/Users/biocbuild/bbs-3.10-bioc/R/library/UniProt.ws/unitTests/test_select.R: Error while sourcing C:/Users/biocbuild/bbs-3.10-bioc/R/library/UniProt.ws/unitTests/test_select.R : Error in file(con, "r") : cannot open the connection
FAILURE in test_mapUniprot: Error in checkTrue(dim(res)[1] > 1) : Test not TRUE
Test files with failing tests
test_select.R
C:/Users/biocbuild/bbs-3.10-bioc/R/library/UniProt.ws/unitTests/test_select.R
test_serviceAccessors.R
test_mapUniprot
Error in BiocGenerics:::testPackage("UniProt.ws") :
unit tests failed for package UniProt.ws
Execution halted
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UniProt.ws.Rcheck/examples_i386/UniProt.ws-Ex.timings
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UniProt.ws.Rcheck/examples_x64/UniProt.ws-Ex.timings
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