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This page was generated on 2024-03-27 11:37:27 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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

Package 291/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellaRepertorium 1.12.0  (landing page)
Andrew McDavid
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/CellaRepertorium
git_branch: RELEASE_3_18
git_last_commit: eccffbf
git_last_commit_date: 2023-10-24 11:27:39 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for CellaRepertorium on merida1


To the developers/maintainers of the CellaRepertorium package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CellaRepertorium
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CellaRepertorium_1.12.0.tar.gz
StartedAt: 2024-03-26 00:15:09 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 00:20:22 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 313.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CellaRepertorium.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CellaRepertorium_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/CellaRepertorium.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellaRepertorium/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellaRepertorium’ version ‘1.12.0’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ‘.’
plot_cluster_factors: no visible binding for global variable ‘chain’
Undefined global functions or variables:
  . chain x_key__
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/CellaRepertorium/libs/CellaRepertorium.so’:
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
plot_cluster_factors  8.937  0.148   9.502
cluster_logistic_test 7.008  0.344   7.673
canonicalize_cluster  5.916  0.114   6.354
cland                 4.729  0.168   5.451
cluster_plot          4.739  0.070   5.012
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/CellaRepertorium.Rcheck/00check.log’
for details.



Installation output

CellaRepertorium.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CellaRepertorium
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘CellaRepertorium’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cdhit-bombs.cpp -o cdhit-bombs.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:545:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
        int max_diag = 0;
            ^
cdhit-common.cpp:669:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
        int max_diag = 0;
            ^
cdhit-common.cpp:2379:9: warning: variable 'mem' set but not used [-Wunused-but-set-variable]
        size_t mem, mega = 1000000;
               ^
cdhit-common.cpp:2993:9: warning: variable 'total_letters' set but not used [-Wunused-but-set-variable]
        size_t total_letters = total_letter;
               ^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cdhit-est.cpp -o cdhit-est.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cdhit.cpp -o cdhit.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c progress.cpp -o progress.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.3-x86_64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 4 | SKIP 0 | PASS 81 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 81 ]
> 
> proc.time()
   user  system elapsed 
 44.098   1.526  47.230 

Example timings

CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings

nameusersystemelapsed
ContigCellDB-fun0.3660.0170.402
canonicalize_cell0.5830.0220.640
canonicalize_cluster5.9160.1146.354
cash-ContigCellDB-method0.2820.0360.329
ccdb_join0.0850.0080.096
cdhit0.2550.1100.393
cdhit_ccdb0.2300.0370.275
cland4.7290.1685.451
cluster_filterset0.0000.0000.001
cluster_germline0.1450.0090.165
cluster_logistic_test7.0080.3447.673
cluster_permute_test1.7610.0351.882
cluster_plot4.7390.0705.012
cross_tab_tbl0.2210.0030.235
crosstab_by_celltype0.1910.0060.203
entropy0.0050.0010.005
enumerate_pairing1.0830.0151.145
equalize_ccdb0.1090.0040.118
fancy_name_contigs0.6960.0500.780
fine_cluster_seqs0.0550.0040.062
fine_clustering3.8340.0344.024
generate_pseudobulk0.3010.0070.315
guess_celltype0.0690.0060.081
hushWarning0.0010.0000.002
left_join_warn0.0320.0230.056
map_axis_labels0.3880.0060.414
mutate_cdb0.1960.0110.212
pairing_tables0.7760.0100.820
plot_cluster_factors8.9370.1489.502
purity0.0010.0010.001
rank_prevalence_ccdb0.6700.0080.731
rbind-ContigCellDB-method0.2180.0070.249
split_cdb0.1090.0050.130
sub-sub-ContigCellDB-character-missing-method0.0810.0180.106