| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:05 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the GeneAccord package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneAccord.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 707/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneAccord 1.10.0 (landing page) Ariane L. Moore
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: GeneAccord |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAccord.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneAccord_1.10.0.tar.gz |
| StartedAt: 2021-10-14 23:27:54 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:31:55 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 240.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneAccord.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneAccord.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GeneAccord_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GeneAccord.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneAccord/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneAccord' version '1.10.0'
* 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 'GeneAccord' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 3.0Mb
extdata 2.1Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 '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-3.13-bioc/meat/GeneAccord.Rcheck/00check.log'
for details.
GeneAccord.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GeneAccord_1.10.0.tar.gz && rm -rf GeneAccord.buildbin-libdir && mkdir GeneAccord.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneAccord.buildbin-libdir GeneAccord_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GeneAccord_1.10.0.zip && rm GeneAccord_1.10.0.tar.gz GeneAccord_1.10.0.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
50 2735k 50 1377k 0 0 1531k 0 0:00:01 --:--:-- 0:00:01 1530k
100 2735k 100 2735k 0 0 1848k 0 0:00:01 0:00:01 --:--:-- 1849k
install for i386
* installing *source* package 'GeneAccord' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeneAccord'
finding HTML links ... done
GeneAccord html
all_genes_tbl html
avg_rates_m html
build_null_test_statistic html
clone_tbl_all_pats_all_trees html
compute_rates_clon_excl html
compute_test_stat_avg_rate html
convert_ensembl_to_reactome_pw_tbl html
create_ensembl_gene_tbl_hg html
create_tbl_ent_clones html
create_tbl_tree_collection html
ecdf_list html
ecdf_lr_test_clon_excl_avg_rate html
ensembl_to_hgnc html
ensembl_to_reactome html
ensg_reactome_path_map html
ensmusg_reactome_path_map html
extract_num_clones_tbl html
generate_ecdf_test_stat html
generate_test_stat_hist html
get_hist_clon_excl html
get_hist_clon_excl_this_pat_this_pair html
get_rate_diff_branch_ent_pair html
heatmap_clones_gene_pat html
hgnc_to_ensembl html
is_diff_branch_ent_pair html
list_of_clon_excl_all_pats html
list_of_num_trees_all_pats html
map_pairs_to_hgnc_symbols html
merge_clones_identical_ents html
pairs_in_patients_hist html
plot_ecdf_test_stat html
plot_rates_clon_excl html
take_pairs_and_get_patients html
vis_pval_distr_num_pat html
write_res_pairs_to_disk 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 'GeneAccord' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneAccord' as GeneAccord_1.10.0.zip
* DONE (GeneAccord)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GeneAccord' successfully unpacked and MD5 sums checked
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GeneAccord.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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.
> library("testthat")
> library("assertthat")
>
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
>
> test_check("GeneAccord")
== Skipped tests ===============================================================
* empty test (15)
[ FAIL 0 | WARN 1 | SKIP 15 | PASS 27 ]
>
>
> proc.time()
user system elapsed
13.79 0.64 14.42
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GeneAccord.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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.
> library("testthat")
> library("assertthat")
>
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
>
> test_check("GeneAccord")
== Skipped tests ===============================================================
* empty test (15)
[ FAIL 0 | WARN 1 | SKIP 15 | PASS 27 ]
>
>
> proc.time()
user system elapsed
16.03 0.40 16.42
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GeneAccord.Rcheck/examples_i386/GeneAccord-Ex.timings
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GeneAccord.Rcheck/examples_x64/GeneAccord-Ex.timings
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