Marc Carlson
| Snapshot Date: 2019-04-11 17:01:57 -0400 (Thu, 11 Apr 2019) |
| URL: https://git.bioconductor.org/packages/UniProt.ws |
| Branch: RELEASE_3_8 |
| Last Commit: dd22a96 |
| Last Changed Date: 2018-10-30 11:41:50 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-12 11:22:47 -0400 (Fri, 12 Apr 2019).
| Package 1611/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| UniProt.ws 2.22.0 Marc Carlson
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: UniProt.ws |
| Version: 2.22.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UniProt.ws.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings UniProt.ws_2.22.0.tar.gz |
| StartedAt: 2019-04-12 06:14:44 -0400 (Fri, 12 Apr 2019) |
| EndedAt: 2019-04-12 06:33:08 -0400 (Fri, 12 Apr 2019) |
| EllapsedTime: 1103.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: UniProt.ws.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UniProt.ws.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings UniProt.ws_2.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/UniProt.ws.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 'UniProt.ws/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'UniProt.ws' version '2.22.0'
* 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 '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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
UniProtWS-class 6.03 0.34 210.17
colsAndKeytypes 2.85 0.02 64.19
utilities 0.75 0.06 6.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
UniProtWS-class 4.89 0.25 226.02
colsAndKeytypes 1.93 0.01 71.76
utilities 0.78 0.04 7.66
* 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:
1 Test Suite :
UniProt.ws RUnit Tests - 20 test functions, 1 error, 0 failures
ERROR in test_newTaxId: Error in file(con, "r") : cannot open the connection
Test files with failing tests
test_select.R
test_newTaxId
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'
OK
* 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
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/UniProt.ws.Rcheck/00check.log'
for details.
UniProt.ws.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/UniProt.ws_2.22.0.tar.gz && rm -rf UniProt.ws.buildbin-libdir && mkdir UniProt.ws.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=UniProt.ws.buildbin-libdir UniProt.ws_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL UniProt.ws_2.22.0.zip && rm UniProt.ws_2.22.0.tar.gz UniProt.ws_2.22.0.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 671k 100 671k 0 0 15.5M 0 --:--:-- --:--:-- --:--:-- 16.8M
install for i386
* installing *source* package 'UniProt.ws' ...
** 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
In R CMD INSTALL
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_2.22.0.zip
* DONE (UniProt.ws)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'UniProt.ws' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
UniProt.ws.Rcheck/tests_i386/UniProt.ws_unit_tests.Rout.fail
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Timing stopped at: 0 0 18.97
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") : InternetOpenUrl failed: 'The operation timed out'
Getting mapping data for P31946 ... and UNIGENE_ID
Getting mapping data for P31946 ... and PDB_ID
Getting extra data for P31946, P62258, Q04917
'select()' returned 1:many mapping between keys and columns
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217, V9HWD8, P01023... (8 total)
'select()' returned 1:many mapping between keys and columns
Getting extra data for P31946, P62258, Q04917
'select()' returned 1:1 mapping between keys and columns
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217, V9HWD8, P01023... (8 total)
'select()' returned 1:many mapping between keys and columns
Getting extra data for Q4LEZ3, Q96SE0, Q9UGJ0... (400 total)
Getting extra data for Q7Z695, Q08AH1, O43306... (400 total)
Getting extra data for O43916, Q9Y4C5, Q7LGC8... (200 total)
'select()' returned 1:1 mapping between keys and columns
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
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
RUNIT TEST PROTOCOL -- Fri Apr 12 06:30:08 2019
***********************************************
Number of test functions: 20
Number of errors: 1
Number of failures: 0
1 Test Suite :
UniProt.ws RUnit Tests - 20 test functions, 1 error, 0 failures
ERROR in test_newTaxId: Error in file(con, "r") : cannot open the connection
Test files with failing tests
test_select.R
test_newTaxId
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
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Getting mapping data for P31946 ... and UNIGENE_ID
Getting mapping data for P31946 ... and PDB_ID
Getting extra data for P31946, P62258, Q04917
'select()' returned 1:many mapping between keys and columns
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217, V9HWD8, P01023... (8 total)
'select()' returned 1:many mapping between keys and columns
Getting extra data for P31946, P62258, Q04917
'select()' returned 1:1 mapping between keys and columns
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217, V9HWD8, P01023... (8 total)
'select()' returned 1:many mapping between keys and columns
Getting extra data for Q4LEZ3, Q96SE0, Q9UGJ0... (400 total)
Getting extra data for Q7Z695, Q08AH1, O43306... (400 total)
Getting extra data for O43916, Q9Y4C5, Q7LGC8... (200 total)
'select()' returned 1:1 mapping between keys and columns
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
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
RUNIT TEST PROTOCOL -- Fri Apr 12 06:33:05 2019
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
UniProt.ws RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
9.09 0.37 176.21
|
|
UniProt.ws.Rcheck/examples_i386/UniProt.ws-Ex.timings
|
UniProt.ws.Rcheck/examples_x64/UniProt.ws-Ex.timings
|