| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:29:53 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the AnnotationForge package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 64/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AnnotationForge 1.32.0 (landing page) Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: AnnotationForge |
| Version: 1.32.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationForge.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AnnotationForge_1.32.0.tar.gz |
| StartedAt: 2021-05-06 00:24:51 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:27:44 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 172.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AnnotationForge.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AnnotationForge.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AnnotationForge_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AnnotationForge.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationForge/DESCRIPTION' ... OK
* this is package 'AnnotationForge' version '1.32.0'
* 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 whether package 'AnnotationForge' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
AnnDbPkg-templates 1.3Mb
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
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'AnnotationForge_unit_tests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/AnnotationForge.Rcheck/00check.log'
for details.
AnnotationForge.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/AnnotationForge_1.32.0.tar.gz && rm -rf AnnotationForge.buildbin-libdir && mkdir AnnotationForge.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AnnotationForge.buildbin-libdir AnnotationForge_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AnnotationForge_1.32.0.zip && rm AnnotationForge_1.32.0.tar.gz AnnotationForge_1.32.0.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 3284k 100 3284k 0 0 48.7M 0 --:--:-- --:--:-- --:--:-- 49.3M
install for i386
* installing *source* package 'AnnotationForge' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'AnnotationForge'
finding HTML links ... done
AnnDbPkg-maker html
finding level-2 HTML links ... done
available.db0pkgs html
generateSeqnames_db html
getProbeDataAffy html
getProbeData_1lq html
makeChipPackageFromDataFrames html
makeInpDb html
makeOrgPackage html
makeOrgPackageFromNCBI html
makeProbePackage html
sqlForge-makeCHIPDB html
sqlForge-popDB html
sqlForge-wrapDBPackages 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 'AnnotationForge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AnnotationForge' as AnnotationForge_1.32.0.zip
* DONE (AnnotationForge)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AnnotationForge' successfully unpacked and MD5 sums checked
|
AnnotationForge.Rcheck/tests_i386/AnnotationForge_unit_tests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> 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, 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
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
[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
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpOCWcLc\fileb706658589e/org.Tguttata.eg.db
Now deleting temporary database file
RUNIT TEST PROTOCOL -- Thu May 06 00:27:21 2021
***********************************************
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 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
8.21 1.18 9.65
|
AnnotationForge.Rcheck/tests_x64/AnnotationForge_unit_tests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> 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, 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
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
[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
Populating go_bp table:
go_bp table filled
Populating go_cc table:
go_cc table filled
Populating go_mf table:
go_mf table filled
'select()' returned many:1 mapping between keys and columns
Populating go_bp_all table:
go_bp_all table filled
Populating go_cc_all table:
go_cc_all table filled
Populating go_mf_all table:
go_mf_all table filled
Populating go_all table:
go_all table filled
Creating package in C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\RtmpmE0PbE\file2268343158c2/org.Tguttata.eg.db
Now deleting temporary database file
RUNIT TEST PROTOCOL -- Thu May 06 00:27:31 2021
***********************************************
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 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
8.39 1.17 9.59
|
|
AnnotationForge.Rcheck/examples_i386/AnnotationForge-Ex.timings
|
AnnotationForge.Rcheck/examples_x64/AnnotationForge-Ex.timings
|