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CHECK report for UniProt.ws on tokay2

This page was generated on 2019-04-08 11:36:46 -0400 (Mon, 08 Apr 2019).

Package 1663/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
UniProt.ws 2.23.0
Marc Carlson
Snapshot Date: 2019-04-07 17:01:41 -0400 (Sun, 07 Apr 2019)
URL: https://git.bioconductor.org/packages/UniProt.ws
Branch: master
Last Commit: 1854923
Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: UniProt.ws
Version: 2.23.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UniProt.ws.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings UniProt.ws_2.23.0.tar.gz
StartedAt: 2019-04-08 06:48:52 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 07:01:44 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 771.8 seconds
RetCode: 0
Status:  OK  
CheckDir: UniProt.ws.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:UniProt.ws.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings UniProt.ws_2.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/UniProt.ws.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '2.23.0'
* 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' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
UniProtWS-class 7.74   0.30  127.24
colsAndKeytypes 4.49   0.01   57.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
UniProtWS-class 7.06   0.28   86.36
colsAndKeytypes 3.30   0.00   57.32
* 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

Installation output

UniProt.ws.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/UniProt.ws_2.23.0.tar.gz && rm -rf UniProt.ws.buildbin-libdir && mkdir UniProt.ws.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=UniProt.ws.buildbin-libdir UniProt.ws_2.23.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL UniProt.ws_2.23.0.zip && rm UniProt.ws_2.23.0.tar.gz UniProt.ws_2.23.0.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  672k  100  672k    0     0  7386k      0 --:--:-- --:--:-- --:--:-- 8101k

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 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_2.23.0.zip
* DONE (UniProt.ws)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'UniProt.ws' successfully unpacked and MD5 sums checked

Tests output

UniProt.ws.Rcheck/tests_i386/UniProt.ws_unit_tests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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, 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 V9JGI4, Q7GXW8, A0A024RBV9... (400 total)
Getting extra data for B4DVF8, H0YH90, Q99809... (400 total)
Getting extra data for J3KS96, A0A0S2A4T3, C7B389... (200 total)
reading url
    https://www.uniprot.org/uniprot/?query=J3KS96+or+A0A0S2A4T3+or+C7B389+or+Q6P2Q0+or+Q7L1H2+or+Q9B2W4+or+Q15H01+or+E5FQ58+or+D1MAM2+or+D3VVP1+or+D3YTF8+or+D5FHN9+or+B2R5W2+or+Q8NCX5+or+Q8NDE0+or+Q9NY41+or+A0A0A7C585+or+A0A0A7C5C4+or+A0A0A7C7F0+or+H7BYD0+or+H7C1K6+or+H7C2K3+or+B1AH80+or+Q6PJ34+or+Q6RLD5+or+Q6UXU7+or+Q6ZTH4+or+Q7YNY5+or+H9PEH5+or+A0A024R036+or+Q76NI6+or+E9PLU7+or+F8VX04+or+L8ECK7+or+M0QXD9+or+M0QXT2+or+M0R027+or+M0R281+or+Q4VYU3+or+A0A3B3IT03+or+Q29844+or+A0A1L4AAN8+or+A0A1X9I3W3+or+A0A024RDE5+or+A0A0G2JIC6+or+Q5TLG3+or+Q9B1A3+or+H3BM89+or+E9PJ14+or+B0YJC5+or+A0A1X9I588+or+R4GMN0+or+A0A024R098+or+Q9UNR6+or+A0A3B3IS19+or+B2RB02+or+B2RD51+or+B2Z8W4+or+B3CJD5+or+B4DGN4+or+E5RH69+or+G8YY13+or+J3QKU2+or+J3QLI8+or+Q4EZ86+or+Q4LE36+or+G9LLY5+or+A0A023QQ48+or+E7EPT0+or+H7C285+or+J3QR88+or+H3BQZ7+or+W0S4B9+or+A0A024RDG9+or+A0A3B3ITP3+or+B9EDF6+or+A0A024R601+or+A0A2R8Y5S3+or+H7C389+or+H7C404+or+H7C4B9+or+O00243+or+O19608+or+O46698+or+Q5DUF5+or+Q6FI30+or+F5GXT8+or+Q9NNY7+or+U5YBL1+or+U5YBR6+or+B4DMP5+or+B4DWV9+or+B4E2M1+or+C9JTY6+or+Q6DV47+or+B3VRX0+or+A0A024RCG7+or+B4DIX7+or+B4DPA5+or+B4DUZ0+or+A0A1K0FU49+or+B2RB70+or+Q59H27+or+Q96K08+or+A0A0A0PVE0+or+A0A0A0WB92+or+A0A186VN23+or+A0A186VNE5+or+B7Z1Z8+or+C9IZD0+or+C9J4C7+or+C9J519+or+C9J998+or+C9JC51+or+B4DR61+or+C9JN04+or+C9JNK1+or+C9JV99+or+B4DT28+or+F6S4E6+or+Q86U79+or+Q86WE6+or+U3N7V6+or+U3PXW9+or+G3V1E0+or+H0Y2M6+or+A0A024RBS4+or+A0A0A7C4R8+or+A0A0A7C7Y3+or+Q5VVD0+or+K7WT83+or+A0A0G2JRV3+or+B2XKZ8+or+E9PN85+or+E9PNM3+or+Q5STU3+or+B6ECB5+or+E9PKI6+or+V9HWJ9+or+E7ETN2+or+B7ZL14+or+Q4GDK8+or+A0A140VK17+or+B7ZKQ9+or+C7SJN5+or+L0E7T1+or+Q8HNQ6+or+A0A024R6C4+or+A9UJN3+or+Q9B1F8+or+H6UMI1+or+Q4GEA3+or+A0A024RCM2+or+V9JD42+or+G5E9W0+or+B1AK88+or+A0A024RDA0+or+Q5QHG3+or+A0A343VDE0+or+A0A384NPW7+or+A0A024R1J3+or+A0A1W2PPZ6+or+G3XAP1+or+Q4GL31+or+A0A0D4WQI1+or+A0N0L5+or+B7Z934+or+A0A343LJL6+or+D3DQ64+or+G5E9G0+or+K7EKQ4+or+A0A024R5V3+or+A0A346REB3+or+Q5T4X2+or+A0A024R2A6+or+A0A0S2Z3Y1+or+A0A342YEY0+or+I3Q2Q4+or+G3V0J0+or+G3V4I3+or+A0A087WYQ2+or+I4ENP2+or+A0A024RCS7+or+Q6IAU3+or+A0A024R259+or+A0A0N6W1Y9+or+B7Z3J9+or+Q96HL2+or+G1ENG5+or+G1EPA2+or+G1EPJ0+or+Q7Z4W0+or+Q96RX4+or+X6R5G7+or+Q6FII3+or+J3KQ70+or+H9P913+or+B7ZLW4+or+A0A1B0GV98+or+A0A1B0GVB4&format=tab&columns=id,sequence
failed on attempt 1 of 5
'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 -- Mon Apr 08 06:59:24 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 
Warning message:
In file(file, "rt") : InternetOpenUrl failed: 'The operation timed out'
> 
> proc.time()
   user  system elapsed 
  13.70    0.70  145.78

UniProt.ws.Rcheck/tests_x64/UniProt.ws_unit_tests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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, 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 V9JGI4, Q7GXW8, A0A024RBV9... (400 total)
Getting extra data for B4DVF8, H0YH90, Q99809... (400 total)
Getting extra data for J3KS96, A0A0S2A4T3, C7B389... (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 -- Mon Apr 08 07:01:15 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 
  12.18    0.45  110.29

Example timings

UniProt.ws.Rcheck/examples_i386/UniProt.ws-Ex.timings

nameusersystemelapsed
UniProtWS-class 7.74 0.30127.24
colsAndKeytypes 4.49 0.0157.94
utilities1.360.021.87

UniProt.ws.Rcheck/examples_x64/UniProt.ws-Ex.timings

nameusersystemelapsed
UniProtWS-class 7.06 0.2886.36
colsAndKeytypes 3.30 0.0057.32
utilities1.210.071.55