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This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the CellaRepertorium package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellaRepertorium.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 257/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellaRepertorium 1.2.0 (landing page) Andrew McDavid
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CellaRepertorium |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2021-10-14 17:09:11 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:12:15 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 184.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CellaRepertorium.Rcheck |
| Warnings: 1 |
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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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CellaRepertorium.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
.git_fetch_output.txt
.git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
cross_tab_tbl: no visible binding for global variable ‘.’
cross_tab_tbl: no visible binding for global variable ‘x_key__’
fancy_name_contigs: no visible binding for global variable ‘.’
pairing_tables: no visible binding for global variable ‘.’
Undefined global functions or variables:
. x_key__
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘cross_tab_tbl’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 4.971 0.21 5.193
* 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/CellaRepertorium.Rcheck/00check.log’
for details.
CellaRepertorium.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CellaRepertorium ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘CellaRepertorium’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-bombs.cpp -o cdhit-bombs.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/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++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit-est.cpp -o cdhit-est.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cdhit.cpp -o cdhit.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c progress.cpp -o progress.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
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 0 | SKIP 0 | PASS 76 ]
>
> proc.time()
user system elapsed
28.816 0.769 29.603
CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings
| name | user | system | elapsed | |
| ContigCellDB-fun | 0.258 | 0.007 | 0.265 | |
| canonicalize_cell | 0.207 | 0.006 | 0.213 | |
| canonicalize_cluster | 4.387 | 0.066 | 4.462 | |
| cash-ContigCellDB-method | 0.203 | 0.008 | 0.212 | |
| ccdb_join | 0.069 | 0.003 | 0.072 | |
| cdhit | 0.249 | 0.067 | 0.319 | |
| cdhit_ccdb | 0.162 | 0.008 | 0.170 | |
| cluster_filterset | 0.001 | 0.000 | 0.000 | |
| cluster_germline | 0.109 | 0.006 | 0.115 | |
| cluster_logistic_test | 4.971 | 0.210 | 5.193 | |
| cluster_permute_test | 0.726 | 0.002 | 0.729 | |
| cluster_plot | 3.496 | 0.052 | 3.598 | |
| crosstab_by_celltype | 0.127 | 0.005 | 0.132 | |
| entropy | 0.003 | 0.001 | 0.003 | |
| enumerate_pairing | 0.527 | 0.005 | 0.532 | |
| equalize_ccdb | 0.101 | 0.002 | 0.104 | |
| fancy_name_contigs | 0.453 | 0.024 | 0.475 | |
| fine_cluster_seqs | 0.040 | 0.003 | 0.042 | |
| fine_clustering | 2.402 | 0.015 | 2.420 | |
| generate_pseudobulk | 0.176 | 0.003 | 0.179 | |
| guess_celltype | 0.055 | 0.004 | 0.058 | |
| hushWarning | 0.000 | 0.000 | 0.001 | |
| left_join_warn | 0.025 | 0.011 | 0.036 | |
| map_axis_labels | 0.198 | 0.004 | 0.202 | |
| mutate_cdb | 0.124 | 0.004 | 0.127 | |
| pairing_tables | 0.578 | 0.004 | 0.582 | |
| purity | 0.000 | 0.001 | 0.001 | |
| rank_prevalence_ccdb | 0.432 | 0.003 | 0.435 | |
| rbind-ContigCellDB-method | 0.107 | 0.003 | 0.111 | |
| split_cdb | 0.062 | 0.003 | 0.064 | |
| sub-sub-ContigCellDB-character-missing-method | 0.054 | 0.008 | 0.063 | |