Andrew McDavid
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/CellaRepertorium |
| Branch: RELEASE_3_12 |
| Last Commit: 4e5b113 |
| Last Changed Date: 2020-10-27 12:03:47 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:29 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the CellaRepertorium package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 249/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellaRepertorium 1.0.0 (landing page) Andrew McDavid
| 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: CellaRepertorium |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellaRepertorium_1.0.0.tar.gz |
| StartedAt: 2021-05-06 00:01:20 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 00:04:11 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 170.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CellaRepertorium.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellaRepertorium_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CellaRepertorium.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellaRepertorium/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellaRepertorium’ version ‘1.0.0’
* 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 ‘CellaRepertorium’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
fancy_name_contigs: no visible binding for global variable ‘.’
pairing_tables: no visible binding for global variable ‘.’
Undefined global functions or variables:
.
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cluster_logistic_test 5.313 0.167 5.494
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/CellaRepertorium.Rcheck/00check.log’
for details.
CellaRepertorium.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CellaRepertorium
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CellaRepertorium’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-common.cpp -o cdhit-common.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:42:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c progress.cpp -o progress.o
In file included from progress.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CellaRepertorium.so RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CellaRepertorium)
CellaRepertorium.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(CellaRepertorium)
>
> test_check("CellaRepertorium")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 73 ]
>
> proc.time()
user system elapsed
28.282 0.781 29.084
CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings
| name | user | system | elapsed | |
| ContigCellDB-fun | 0.232 | 0.010 | 0.241 | |
| canonicalize_cell | 0.229 | 0.005 | 0.234 | |
| canonicalize_cluster | 4.180 | 0.066 | 4.252 | |
| cash-ContigCellDB-method | 0.220 | 0.007 | 0.228 | |
| ccdb_join | 0.063 | 0.004 | 0.067 | |
| cdhit | 0.256 | 0.068 | 0.326 | |
| cdhit_ccdb | 0.164 | 0.011 | 0.175 | |
| cluster_filterset | 0.001 | 0.001 | 0.000 | |
| cluster_germline | 0.114 | 0.004 | 0.118 | |
| cluster_logistic_test | 5.313 | 0.167 | 5.494 | |
| cluster_permute_test | 0.549 | 0.004 | 0.554 | |
| cluster_plot | 3.135 | 0.044 | 3.185 | |
| crosstab_by_celltype | 0.121 | 0.004 | 0.124 | |
| entropy | 0.003 | 0.000 | 0.003 | |
| enumerate_pairing | 0.531 | 0.007 | 0.540 | |
| equalize_ccdb | 0.088 | 0.002 | 0.090 | |
| fancy_name_contigs | 0.215 | 0.020 | 0.237 | |
| fine_cluster_seqs | 0.046 | 0.003 | 0.049 | |
| fine_clustering | 2.620 | 0.018 | 2.640 | |
| generate_pseudobulk | 0.238 | 0.003 | 0.241 | |
| guess_celltype | 0.049 | 0.004 | 0.055 | |
| hushWarning | 0.002 | 0.000 | 0.001 | |
| left_join_warn | 0.028 | 0.014 | 0.042 | |
| map_axis_labels | 0.200 | 0.005 | 0.205 | |
| mutate_cdb | 0.159 | 0.008 | 0.167 | |
| pairing_tables | 0.566 | 0.003 | 0.569 | |
| purity | 0.000 | 0.000 | 0.001 | |
| rank_prevalence_ccdb | 0.497 | 0.004 | 0.502 | |
| rbind-ContigCellDB-method | 0.140 | 0.003 | 0.145 | |
| split_cdb | 0.069 | 0.002 | 0.070 | |
| sub-sub-ContigCellDB-character-missing-method | 0.061 | 0.008 | 0.069 | |