Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:00 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 272/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CellaRepertorium 1.8.0 (landing page) Andrew McDavid
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: CellaRepertorium |
Version: 1.8.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings CellaRepertorium_1.8.0.tar.gz |
StartedAt: 2023-04-10 19:34:12 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:38:03 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 231.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CellaRepertorium.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings CellaRepertorium_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/CellaRepertorium.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘CellaRepertorium/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CellaRepertorium’ version ‘1.8.0’ * 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 ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: libs 3.8Mb * 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 loading without being on the library search path ... 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 ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ... ‘cdr3_clustering.Rmd’ using ‘UTF-8’... OK ‘cr-overview.Rmd’ using ‘UTF-8’... OK ‘mouse_tcell_qc.Rmd’ using ‘UTF-8’... OK ‘repertoire_and_expression.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/CellaRepertorium.Rcheck/00check.log’ for details.
CellaRepertorium.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL CellaRepertorium ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘CellaRepertorium’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cdhit-bombs.cpp -o cdhit-bombs.o In file included from cdhit-bombs.cpp:2: cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’: cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 494 | if( band > options.band_width ) band = options.band_width; | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cdhit-common.cpp -o cdhit-common.o cdhit-common.cpp:160: warning: ignoring #pragma omp critical [-Wunknown-pragmas] 160 | #pragma omp critical | cdhit-common.cpp:174: warning: ignoring #pragma omp critical [-Wunknown-pragmas] 174 | #pragma omp critical | cdhit-common.cpp:2418: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] 2418 | #pragma omp parallel for schedule( dynamic, 1 ) | cdhit-common.cpp:2435: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] 2435 | #pragma omp parallel for schedule( dynamic, 1 ) | cdhit-common.cpp:2437: warning: ignoring #pragma omp flush [-Wunknown-pragmas] 2437 | #pragma omp flush (stop) | cdhit-common.cpp:2458: warning: ignoring #pragma omp critical [-Wunknown-pragmas] 2458 | #pragma omp critical | cdhit-common.cpp:2467: warning: ignoring #pragma omp flush [-Wunknown-pragmas] 2467 | #pragma omp flush (stop) | cdhit-common.cpp:2492: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] 2492 | #pragma omp parallel for schedule( dynamic, 1 ) | cdhit-common.cpp:3151: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] 3151 | #pragma omp parallel for schedule( dynamic, 1 ) | In file included from cdhit-common.cpp:37: cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’: cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 494 | if( band > options.band_width ) band = options.band_width; | ~~~~~^~~~~~~~~~~~~~~~~~~~ cdhit-common.cpp: In function ‘int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)’: cdhit-common.cpp:545:6: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable] 545 | int max_diag = 0; | ^~~~~~~~ cdhit-common.cpp: In function ‘int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)’: cdhit-common.cpp:669:6: warning: variable ‘max_diag’ set but not used [-Wunused-but-set-variable] 669 | int max_diag = 0; | ^~~~~~~~ cdhit-common.cpp: In member function ‘void SequenceDB::SortDivide(Options&, bool)’: cdhit-common.cpp:1774:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1774 | if (len > max_len) max_len = len; | ~~~~^~~~~~~~~ cdhit-common.cpp:1775:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1775 | if (len < min_len) min_len = len; | ~~~~^~~~~~~~~ cdhit-common.cpp: In member function ‘void SequenceDB::DoClustering(int, const Options&)’: cdhit-common.cpp:2379:9: warning: variable ‘mem’ set but not used [-Wunused-but-set-variable] 2379 | size_t mem, mega = 1000000; | ^~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cdhit-est.cpp -o cdhit-est.o In file included from cdhit-est.cpp:32: cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’: cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 494 | if( band > options.band_width ) band = options.band_width; | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cdhit.cpp -o cdhit.o In file included from cdhit.cpp:31: cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’: cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 494 | if( band > options.band_width ) band = options.band_width; | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c progress.cpp -o progress.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o CellaRepertorium.so RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 22.864 1.060 23.909
CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings
name | user | system | elapsed | |
ContigCellDB-fun | 0.181 | 0.008 | 0.189 | |
canonicalize_cell | 0.279 | 0.000 | 0.279 | |
canonicalize_cluster | 3.095 | 0.124 | 3.219 | |
cash-ContigCellDB-method | 0.176 | 0.016 | 0.191 | |
ccdb_join | 0.039 | 0.008 | 0.047 | |
cdhit | 0.246 | 0.152 | 0.398 | |
cdhit_ccdb | 0.117 | 0.012 | 0.129 | |
cland | 3.759 | 0.140 | 3.899 | |
cluster_filterset | 0 | 0 | 0 | |
cluster_germline | 0.075 | 0.000 | 0.075 | |
cluster_logistic_test | 3.630 | 0.123 | 3.755 | |
cluster_permute_test | 0.845 | 0.033 | 0.878 | |
cluster_plot | 2.166 | 0.100 | 2.266 | |
cross_tab_tbl | 0.089 | 0.003 | 0.093 | |
crosstab_by_celltype | 0.091 | 0.004 | 0.095 | |
entropy | 0.002 | 0.001 | 0.002 | |
enumerate_pairing | 0.462 | 0.000 | 0.462 | |
equalize_ccdb | 0.061 | 0.000 | 0.061 | |
fancy_name_contigs | 0.314 | 0.032 | 0.351 | |
fine_cluster_seqs | 0.026 | 0.004 | 0.030 | |
fine_clustering | 1.874 | 0.060 | 1.934 | |
generate_pseudobulk | 0.137 | 0.000 | 0.137 | |
guess_celltype | 0.038 | 0.000 | 0.038 | |
hushWarning | 0.001 | 0.000 | 0.001 | |
left_join_warn | 0.016 | 0.000 | 0.016 | |
map_axis_labels | 0.21 | 0.00 | 0.21 | |
mutate_cdb | 0.105 | 0.004 | 0.110 | |
pairing_tables | 0.547 | 0.016 | 0.563 | |
plot_cluster_factors | 4.191 | 0.088 | 4.278 | |
purity | 0.000 | 0.000 | 0.001 | |
rank_prevalence_ccdb | 0.323 | 0.008 | 0.331 | |
rbind-ContigCellDB-method | 0.21 | 0.00 | 0.21 | |
split_cdb | 0.064 | 0.004 | 0.067 | |
sub-sub-ContigCellDB-character-missing-method | 0.042 | 0.004 | 0.045 | |