| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:37 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
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To the developers/maintainers of the GenomeInfoDb package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomeInfoDb.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 745/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomeInfoDb 1.30.1 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: GenomeInfoDb |
| Version: 1.30.1 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.30.1.tar.gz |
| StartedAt: 2022-04-12 20:12:57 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 20:32:46 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1188.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomeInfoDb.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.30.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomeInfoDb.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomeInfoDb/DESCRIPTION' ... OK
* this is package 'GenomeInfoDb' version '1.30.1'
* 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 'GenomeInfoDb' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
extdata 3.5Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: 'utils:::.roman2numeric'
See the note in ?`:::` about the use of this operator.
* 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' ... ERROR
Running examples in 'GenomeInfoDb-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getChromInfoFromEnsembl
> ### Title: Get chromosome information for an Ensembl species
> ### Aliases: getChromInfoFromEnsembl
> ### Keywords: manip
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. BASIC EXAMPLES
> ## ---------------------------------------------------------------------
>
> ## Internet access required!
>
> ## === Worm ===
> ## https://uswest.ensembl.org/Caenorhabditis_elegans
>
> celegans <- getChromInfoFromEnsembl("celegans")
Error in .attrib_type_codes_to_ids_from_Ensembl_FTP(core_db_url, codes) :
table "attrib_type" has no entry for: toplevel
Calls: getChromInfoFromEnsembl ... .fetch_attribs_from_Ensembl_FTP -> .attrib_type_codes_to_ids_from_Ensembl_FTP
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GenomeInfoDb-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getChromInfoFromEnsembl
> ### Title: Get chromosome information for an Ensembl species
> ### Aliases: getChromInfoFromEnsembl
> ### Keywords: manip
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## A. BASIC EXAMPLES
> ## ---------------------------------------------------------------------
>
> ## Internet access required!
>
> ## === Worm ===
> ## https://uswest.ensembl.org/Caenorhabditis_elegans
>
> celegans <- getChromInfoFromEnsembl("celegans")
Error in .attrib_type_codes_to_ids_from_Ensembl_FTP(core_db_url, codes) :
table "attrib_type" has no entry for: toplevel
Calls: getChromInfoFromEnsembl ... .fetch_attribs_from_Ensembl_FTP -> .attrib_type_codes_to_ids_from_Ensembl_FTP
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.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: 2 ERRORs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomeInfoDb.Rcheck/00check.log'
for details.
GenomeInfoDb.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GenomeInfoDb_1.30.1.tar.gz && rm -rf GenomeInfoDb.buildbin-libdir && mkdir GenomeInfoDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.30.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenomeInfoDb_1.30.1.zip && rm GenomeInfoDb_1.30.1.tar.gz GenomeInfoDb_1.30.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
24 3091k 24 756k 0 0 750k 0 0:00:04 0:00:01 0:00:03 751k
79 3091k 79 2445k 0 0 1218k 0 0:00:02 0:00:02 --:--:-- 1219k
100 3091k 100 3091k 0 0 1362k 0 0:00:02 0:00:02 --:--:-- 1362k
install for i386
* installing *source* package 'GenomeInfoDb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomeInfoDb'
finding HTML links ... done
GenomeDescription-class html
GenomeInfoDb-internals html
Seqinfo-class html
fetchExtendedChromInfoFromUCSC html
getChromInfoFromEnsembl html
getChromInfoFromNCBI html
getChromInfoFromUCSC html
loadTaxonomyDb html
mapGenomeBuilds html
rankSeqlevels html
seqinfo html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GenomeInfoDb.buildbin-libdir/00LOCK-GenomeInfoDb/00new/GenomeInfoDb/help/seqinfo.html
seqlevels-wrappers html
seqlevelsStyle 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 'GenomeInfoDb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeInfoDb' as GenomeInfoDb_1.30.1.zip
* DONE (GenomeInfoDb)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GenomeInfoDb' successfully unpacked and MD5 sums checked
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GenomeInfoDb.Rcheck/tests_i386/run_unitTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
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
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
[1] TRUE
> GenomeInfoDb:::.test()
RUNIT TEST PROTOCOL -- Tue Apr 12 20:24:16 2022
***********************************************
Number of test functions: 21
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomeInfoDb RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21
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
351.64 16.75 548.34
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GenomeInfoDb.Rcheck/tests_x64/run_unitTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
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
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
[1] TRUE
> GenomeInfoDb:::.test()
RUNIT TEST PROTOCOL -- Tue Apr 12 20:32:37 2022
***********************************************
Number of test functions: 21
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomeInfoDb RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21
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
338.90 15.75 500.15
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GenomeInfoDb.Rcheck/examples_i386/GenomeInfoDb-Ex.timings
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GenomeInfoDb.Rcheck/examples_x64/GenomeInfoDb-Ex.timings
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