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This page was generated on 2021-09-13 15:06:52 -0400 (Mon, 13 Sep 2021).

CHECK results for CellaRepertorium on machv2

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.

raw results

Package 257/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellaRepertorium 1.2.0  (landing page)
Andrew McDavid
Snapshot Date: 2021-09-12 04:50:10 -0400 (Sun, 12 Sep 2021)
git_url: https://git.bioconductor.org/packages/CellaRepertorium
git_branch: RELEASE_3_13
git_last_commit: 86b7f10
git_last_commit_date: 2021-05-19 12:57:31 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

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: 2021-09-12 17:04:40 -0400 (Sun, 12 Sep 2021)
EndedAt: 2021-09-12 17:07:43 -0400 (Sun, 12 Sep 2021)
EllapsedTime: 183.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CellaRepertorium.Rcheck
Warnings: 1

Command output

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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 5.114  0.206   5.379
* 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.



Installation output

CellaRepertorium.Rcheck/00install.out

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###
### 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)

Tests output

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 
 28.049   0.741  28.788 

Example timings

CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings

nameusersystemelapsed
ContigCellDB-fun0.2780.0120.290
canonicalize_cell0.1920.0050.197
canonicalize_cluster3.8390.0563.896
cash-ContigCellDB-method0.1540.0060.159
ccdb_join0.0660.0060.072
cdhit0.2530.0660.320
cdhit_ccdb0.1350.0110.146
cluster_filterset0.0010.0010.000
cluster_germline0.0820.0050.087
cluster_logistic_test5.1140.2065.379
cluster_permute_test0.6080.0040.612
cluster_plot3.2710.0493.324
crosstab_by_celltype0.1070.0030.111
entropy0.0030.0000.004
enumerate_pairing0.5450.0030.548
equalize_ccdb0.0940.0030.097
fancy_name_contigs1.1170.0431.157
fine_cluster_seqs0.0340.0010.035
fine_clustering2.5330.0162.551
generate_pseudobulk0.2350.0040.240
guess_celltype0.0570.0040.061
hushWarning0.0010.0000.001
left_join_warn0.0290.0150.045
map_axis_labels0.2160.0030.220
mutate_cdb0.1300.0060.136
pairing_tables0.5080.0050.513
purity0.0010.0000.000
rank_prevalence_ccdb0.3770.0040.380
rbind-ContigCellDB-method0.1530.0030.157
split_cdb0.0960.0040.099
sub-sub-ContigCellDB-character-missing-method0.0530.0080.061