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This page was generated on 2022-01-17 11:12:19 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for UniProt.ws on merida1


To the developers/maintainers of the UniProt.ws package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/UniProt.ws.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2021/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
UniProt.ws 2.35.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/UniProt.ws
git_branch: master
git_last_commit: bd5237b
git_last_commit_date: 2021-10-26 12:05:27 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: UniProt.ws
Version: 2.35.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UniProt.ws_2.35.0.tar.gz
StartedAt: 2022-01-17 06:54:38 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 07:01:05 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 386.4 seconds
RetCode: 0
Status:   OK  
CheckDir: UniProt.ws.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings UniProt.ws_2.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/UniProt.ws.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.35.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
UniProtWS-class 2.911  0.135  57.314
colsAndKeytypes 0.322  0.027  26.422
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/UniProt.ws.Rcheck/00check.log’
for details.



Installation output

UniProt.ws.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL UniProt.ws
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘UniProt.ws’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (UniProt.ws)

Tests output

UniProt.ws.Rcheck/tests/UniProt.ws_unit_tests.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: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.max, which.min

Getting mapping data for P31946 ... and PDB_ID
Getting mapping data for P31946 ... and HGNC_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 PDB_ID
Getting mapping data for P04217 ... and HGNC_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 Q96NG5, Q6ZN19, Q9UI25... (100 total)
'select()' returned 1:1 mapping between keys and columns
Getting mapping data for P31946 ... and P_ENTREZGENEID
'select()' returned 1:1 mapping between keys and columns
Getting mapping data for P31946 ... and P_ENTREZGENEID
Getting extra data for P31946, P62258, Q04917
'select()' returned 1:1 mapping between keys and columns
GENEID and ENTREZ_GENE are the same.
  returning only GENEID in results.
Getting mapping data for P31946 ... and P_ENTREZGENEID
Getting extra data for P31946, P62258, Q04917
'select()' returned 1:1 mapping between keys and columns
Getting mapping data for P31946 ... and P_ENTREZGENEID
Getting extra data for P31946, P62258, Q04917
'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 GENENAME


RUNIT TEST PROTOCOL -- Mon Jan 17 07:00:55 2022 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
UniProt.ws RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 12.139   0.609 116.225 

Example timings

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

nameusersystemelapsed
UniProtWS-class 2.911 0.13557.314
colsAndKeytypes 0.322 0.02726.422
utilities1.4980.0623.099