Marc Carlson
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/UniProt.ws |
| Branch: RELEASE_3_7 |
| Last Commit: 1a14832 |
| Last Changed Date: 2018-10-15 16:30:06 -0400 (Mon, 15 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:36:43 -0400 (Wed, 17 Oct 2018).
| Package 1526/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| UniProt.ws 2.20.4 Marc Carlson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: UniProt.ws |
| Version: 2.20.4 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UniProt.ws.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings UniProt.ws_2.20.4.tar.gz |
| StartedAt: 2018-10-17 05:21:01 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:29:18 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 497.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: UniProt.ws.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UniProt.ws.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings UniProt.ws_2.20.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/UniProt.ws.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.20.4'
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
UniProtWS-class 7.46 0.44 62.49
colsAndKeytypes 3.91 0.01 35.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
UniProtWS-class 6.51 0.19 56.73
colsAndKeytypes 3.22 0.00 36.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'UniProt.ws_unit_tests.R'
OK
** 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: OK
UniProt.ws.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/UniProt.ws_2.20.4.tar.gz && rm -rf UniProt.ws.buildbin-libdir && mkdir UniProt.ws.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=UniProt.ws.buildbin-libdir UniProt.ws_2.20.4.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL UniProt.ws_2.20.4.zip && rm UniProt.ws_2.20.4.tar.gz UniProt.ws_2.20.4.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 672k 100 672k 0 0 10.2M 0 --:--:-- --:--:-- --:--:-- 11.5M
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_2.20.4.zip
* DONE (UniProt.ws)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-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
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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
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,P01023,P18440,A4Z6T7
'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,P01023,P18440,A4Z6T7
'select()' returned 1:many mapping between keys and columns
Getting extra data for A0A2U8RNL1,A0A2U8J924,A0A2U8LMN2,A0A1S5UZ15,A0A2X0SFL7,Q96JJ8
Getting extra data for A6YZ48,Q8WY19,Q6FHX6,D9YZU8,E9PG39,D3DQ30
Getting extra data for Q9GZT9,P49411,Q06889,Q96D98,P17813,Q96KQ7
'select()' returned 1:1 mapping between keys and columns
Getting extra data for P04217,P30443
Getting extra data for P13368,P20806,Q9UM73,P97793,Q17192
Getting extra data for P13368,P20806,Q9UM73,P97793,Q17192
Getting mapping data for P13368 ... and P_REFSEQ_AC
Getting mapping data for P04217 ... and UNIGENE_ID
RUNIT TEST PROTOCOL -- Wed Oct 17 05:27:23 2018
***********************************************
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
Warning messages:
1: In matrix(vec2, ncol = 2, byrow = TRUE) :
data length [81] is not a sub-multiple or multiple of the number of rows [41]
2: In matrix(vec2, ncol = 2, byrow = TRUE) :
data length [81] is not a sub-multiple or multiple of the number of rows [41]
>
> proc.time()
user system elapsed
13.01 0.67 83.23
|
UniProt.ws.Rcheck/tests_x64/UniProt.ws_unit_tests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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,P01023,P18440,A4Z6T7
'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,P01023,P18440,A4Z6T7
'select()' returned 1:many mapping between keys and columns
Getting extra data for A0A2U8RNL1,A0A2U8J924,A0A2U8LMN2,A0A1S5UZ15,A0A2X0SFL7,Q96JJ8
Getting extra data for A6YZ48,Q8WY19,Q6FHX6,D9YZU8,E9PG39,D3DQ30
Getting extra data for Q9GZT9,P49411,Q06889,Q96D98,P17813,Q96KQ7
'select()' returned 1:1 mapping between keys and columns
Getting extra data for P04217,P30443
Getting extra data for P13368,P20806,Q9UM73,P97793,Q17192
Getting extra data for P13368,P20806,Q9UM73,P97793,Q17192
Getting mapping data for P13368 ... and P_REFSEQ_AC
Getting mapping data for P04217 ... and UNIGENE_ID
RUNIT TEST PROTOCOL -- Wed Oct 17 05:29:12 2018
***********************************************
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
Warning messages:
1: In matrix(vec2, ncol = 2, byrow = TRUE) :
data length [81] is not a sub-multiple or multiple of the number of rows [41]
2: In matrix(vec2, ncol = 2, byrow = TRUE) :
data length [81] is not a sub-multiple or multiple of the number of rows [41]
3: In file(file, "rt") : InternetOpenUrl failed: 'The operation timed out'
>
> proc.time()
user system elapsed
11.70 0.39 109.45
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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
|