| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:44 -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 immunotation package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/immunotation.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 927/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| immunotation 1.2.0 (landing page) Katharina Imkeller
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: immunotation |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:immunotation.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings immunotation_1.2.0.tar.gz |
| StartedAt: 2022-04-12 21:24:47 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 21:30:51 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 363.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: immunotation.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:immunotation.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings immunotation_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/immunotation.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 'immunotation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'immunotation' version '1.2.0'
* 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 'immunotation' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
R 3.8Mb
extdata 2.2Mb
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_allele_frequency 3.91 0.19 18.64
query_haplotype_frequencies 0.79 0.12 14.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_allele_frequency 3.61 0.36 14.32
query_haplotype_frequencies 0.79 0.08 10.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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-3.14-bioc/meat/immunotation.Rcheck/00check.log'
for details.
immunotation.Rcheck/00install.out
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###
### Running command:
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### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/immunotation_1.2.0.tar.gz && rm -rf immunotation.buildbin-libdir && mkdir immunotation.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=immunotation.buildbin-libdir immunotation_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL immunotation_1.2.0.zip && rm immunotation_1.2.0.tar.gz immunotation_1.2.0.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
31 1676k 31 532k 0 0 789k 0 0:00:02 --:--:-- 0:00:02 788k
100 1676k 100 1676k 0 0 1181k 0 0:00:01 0:00:01 --:--:-- 1182k
install for i386
* installing *source* package 'immunotation' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'immunotation'
finding HTML links ... done
assemble_protein_complex html
build_allele_group html
check_geographics html
check_hla_locus html
check_hla_selection html
check_population html
check_sample_size html
check_standard html
create_encode_handle html
decode_MAC html
encode_MAC html
extract_population_id html
extract_population_info html
extract_population_name html
extract_sample_info html
fetch_encoded_MAC html
getURL html
get_G_group html
get_P_group html
get_external_file html
get_mhcpan_input html
get_nb_pages html
get_serotypes html
get_valid_geographics html
get_valid_organisms html
human_protein_complex_table html
load_mro html
mro.obo html
parse_allele_freq_html html
parse_haplotype_freq_html html
plot_allele_frequency html
query_allele_frequencies html
query_haplotype_frequencies html
query_population_detail html
read_complete_freq_table html
read_population_detail html
retrieve_chain_lookup_table html
verify_parameters 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 'immunotation' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'immunotation' as immunotation_1.2.0.zip
* DONE (immunotation)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'immunotation' successfully unpacked and MD5 sums checked
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immunotation.Rcheck/tests_i386/testthat.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.
> library(testthat)
> library(immunotation)
>
> test_check("immunotation")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 146 ]
Warning messages:
1: In for (i in seq_len(n)) { :
closing unused connection 9 (https://iamnotanurl)
2: In for (i in seq_len(n)) { :
closing unused connection 8 (https://iamnotanurl)
3: In for (i in seq_len(n)) { :
closing unused connection 6 (https://iamnotanurl)
4: In .Internal(lapply(X, FUN)) :
closing unused connection 5 (https://iamnotanurl)
5: In .Internal(lapply(X, FUN)) :
closing unused connection 4 (https://iamnotanurl)
>
>
> proc.time()
user system elapsed
55.09 0.85 98.28
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immunotation.Rcheck/tests_x64/testthat.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.
> library(testthat)
> library(immunotation)
>
> test_check("immunotation")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 146 ]
Warning messages:
1: In for (i in seq_len(n)) { :
closing unused connection 9 (https://iamnotanurl)
2: In for (i in seq_len(n)) { :
closing unused connection 8 (https://iamnotanurl)
3: In for (i in seq_len(n)) { :
closing unused connection 6 (https://iamnotanurl)
4: In .Internal(lapply(X, FUN)) :
closing unused connection 5 (https://iamnotanurl)
5: In .Internal(lapply(X, FUN)) :
closing unused connection 4 (https://iamnotanurl)
>
>
> proc.time()
user system elapsed
62.54 0.82 99.34
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immunotation.Rcheck/examples_i386/immunotation-Ex.timings
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immunotation.Rcheck/examples_x64/immunotation-Ex.timings
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