Package: UniProt.ws

Version: 2.20.4

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings UniProt.ws_2.20.4.tar.gz

StartedAt: 2018-10-16 04:22:52 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 04:27:37 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 284.3 seconds

RetCode: 0

Status:  OK

CheckDir: UniProt.ws.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings UniProt.ws_2.20.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/UniProt.ws.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
UniProtWS-class 1.628  0.112  94.682
colsAndKeytypes 0.448  0.056  36.936
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL UniProt.ws
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘UniProt.ws’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (UniProt.ws)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Tue Oct 16 04:27:34 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 
  6.260   0.344  91.230 

name	user	system	elapsed
UniProtWS-class	1.628	0.112	94.682
colsAndKeytypes	0.448	0.056	36.936
utilities	0.604	0.000	0.601