| Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-16 11:49:36 -0400 (Tue, 16 Apr 2019).
| Package 56/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| AnnotationForge 1.24.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] |  | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: AnnotationForge |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AnnotationForge.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AnnotationForge_1.24.0.tar.gz |
| StartedAt: 2019-04-15 22:11:56 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:13:33 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 96.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AnnotationForge.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AnnotationForge.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AnnotationForge_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/AnnotationForge.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.24.0’
* 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-3.8-bioc/meat/AnnotationForge.Rcheck/00check.log’
for details.
AnnotationForge.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL AnnotationForge ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-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)
AnnotationForge.Rcheck/tests/AnnotationForge_unit_tests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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/RtmpkyhL7e/file64ee1316eb30/org.Tguttata.eg.db
Now deleting temporary database file
RUNIT TEST PROTOCOL -- Mon Apr 15 22:13:30 2019
***********************************************
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
7.580 0.296 7.981
AnnotationForge.Rcheck/AnnotationForge-Ex.timings
| name | user | system | elapsed | |
| AnnDbPkg-maker | 0.052 | 0.008 | 0.080 | |
| available.db0pkgs | 0.120 | 0.000 | 0.296 | |
| generateSeqnames_db | 0 | 0 | 0 | |
| getProbeDataAffy | 0 | 0 | 0 | |
| getProbeData_1lq | 0.000 | 0.004 | 0.000 | |
| makeChipPackageFromDataFrames | 0.000 | 0.000 | 0.002 | |
| makeInpDb | 0.004 | 0.000 | 0.000 | |
| makeOrgPackage | 0.004 | 0.000 | 0.005 | |
| makeOrgPackageFromNCBI | 0 | 0 | 0 | |
| makeProbePackage | 2.392 | 0.052 | 2.487 | |
| sqlForge-makeCHIPDB | 0 | 0 | 0 | |
| sqlForge-popDB | 0 | 0 | 0 | |
| sqlForge-wrapDBPackages | 0 | 0 | 0 | |