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CHECK report for AnnotationForge on malbec2

This page was generated on 2018-06-25 10:02:34 -0400 (Mon, 25 Jun 2018).

Package 53/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationForge 1.22.0
Bioconductor Package Maintainer
Snapshot Date: 2018-06-24 16:46:06 -0400 (Sun, 24 Jun 2018)
URL: https://git.bioconductor.org/packages/AnnotationForge
Branch: RELEASE_3_7
Last Commit: 65f30b8
Last Changed Date: 2018-04-30 10:35:25 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationForge
Version: 1.22.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:AnnotationForge.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings AnnotationForge_1.22.0.tar.gz
StartedAt: 2018-06-24 22:19:11 -0400 (Sun, 24 Jun 2018)
EndedAt: 2018-06-24 22:20:29 -0400 (Sun, 24 Jun 2018)
EllapsedTime: 77.7 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationForge.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:AnnotationForge.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings AnnotationForge_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/AnnotationForge.Rcheck’
* using R version 3.5.0 (2018-04-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* this is package ‘AnnotationForge’ version ‘1.22.0’
* package encoding: UTF-8
* 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 ‘AnnotationForge’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.7Mb
    extdata              3.3Mb
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationForge_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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/AnnotationForge.Rcheck/00check.log’
for details.



Installation output

AnnotationForge.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL AnnotationForge
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘AnnotationForge’ ...
** 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 (AnnotationForge)

Tests output

AnnotationForge.Rcheck/tests/AnnotationForge_unit_tests.Rout


R version 3.5.0 (2018-04-23) -- "Joy in Playing"
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.

> require("AnnotationForge") || stop("unable to load AnnotationForge package")
Loading required package: AnnotationForge
Loading required package: BiocGenerics
Loading required package: parallel

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

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

[1] TRUE
> AnnotationForge:::.test()

'select()' returned many:1 mapping between keys and columns
'select()' returned many:1 mapping between keys and columns
Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating chromosome table:
chromosome table filled
Populating go table:
go table filled
table metadata filled
'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
'select()' returned many:1 mapping between keys and columns
Populating go_all table:
go_all table filled
Creating package in /tmp/RtmpGsQS6F/file582b5a6f5ae0/org.Tguttata.eg.db 
Now deleting temporary database file


RUNIT TEST PROTOCOL -- Sun Jun 24 22:20:26 2018 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationForge RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
There were 40 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  5.964   0.308   6.522 

Example timings

AnnotationForge.Rcheck/AnnotationForge-Ex.timings

nameusersystemelapsed
AnnDbPkg-maker0.0280.0080.045
available.db0pkgs0.0800.0000.298
generateSeqnames_db000
getProbeDataAffy0.0000.0000.001
getProbeData_1lq000
makeChipPackageFromDataFrames0.0000.0000.003
makeInpDb0.0040.0000.000
makeOrgPackage0.0040.0000.004
makeOrgPackageFromNCBI000
makeProbePackage2.2800.0842.881
sqlForge-makeCHIPDB0.0000.0040.002
sqlForge-popDB0.0040.0000.003
sqlForge-wrapDBPackages0.0000.0000.001