Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:30 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 291/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CellaRepertorium 1.12.0 (landing page) Andrew McDavid
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: CellaRepertorium |
Version: 1.12.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CellaRepertorium_1.12.0.tar.gz |
StartedAt: 2023-11-02 09:03:58 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 09:07:13 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 195.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CellaRepertorium.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CellaRepertorium_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CellaRepertorium.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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: ‘g++ (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: libs 3.5Mb * 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 ... WARNING Note: information on .o files is not available File ‘/home/biocbuild/R/R-4.3.1/site-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 5.574 0.095 5.787 canonicalize_cluster 4.133 0.837 5.181 cluster_logistic_test 4.747 0.173 5.043 * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/CellaRepertorium.Rcheck/00check.log’ for details.
CellaRepertorium.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL CellaRepertorium ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘CellaRepertorium’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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; | ^~~ In file included from cdhit-common.cpp:37: In member function ‘void NVector<TYPE>::Resize(int, const TYPE&) [with TYPE = long int]’, inlined from ‘NVector<TYPE>::NVector(int, const TYPE&) [with TYPE = long int]’ at cdhit-common.h:124:10, inlined from ‘int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)’ at cdhit-common.cpp:802:36: cdhit-common.h:149:27: warning: argument 1 range [18446744056529682448, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 149 | items = (TYPE*)realloc( items, capacity*sizeof(TYPE) ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cdhit-common.h: In function ‘int local_band_align(char*, char*, int, int, ScoreMatrix&, int&, int&, int&, float&, int*, int, int, int, WorkingBuffer&)’: cdhit-common.h:149:27: note: in a call to built-in allocation function ‘void* __builtin_malloc(long unsigned int)’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c progress.cpp -o progress.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 29.832 4.630 38.042
CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings
name | user | system | elapsed | |
ContigCellDB-fun | 0.240 | 0.000 | 0.243 | |
canonicalize_cell | 0.364 | 0.008 | 0.374 | |
canonicalize_cluster | 4.133 | 0.837 | 5.181 | |
cash-ContigCellDB-method | 0.181 | 0.010 | 0.195 | |
ccdb_join | 0.053 | 0.000 | 0.054 | |
cdhit | 0.267 | 0.157 | 0.438 | |
cdhit_ccdb | 0.173 | 0.027 | 0.204 | |
cland | 3.992 | 0.153 | 4.199 | |
cluster_filterset | 0 | 0 | 0 | |
cluster_germline | 0.085 | 0.012 | 0.097 | |
cluster_logistic_test | 4.747 | 0.173 | 5.043 | |
cluster_permute_test | 1.167 | 0.015 | 1.203 | |
cluster_plot | 3.031 | 0.099 | 3.152 | |
cross_tab_tbl | 0.138 | 0.000 | 0.142 | |
crosstab_by_celltype | 0.123 | 0.004 | 0.130 | |
entropy | 0.002 | 0.000 | 0.003 | |
enumerate_pairing | 0.596 | 0.031 | 0.637 | |
equalize_ccdb | 0.069 | 0.003 | 0.073 | |
fancy_name_contigs | 0.492 | 0.062 | 0.597 | |
fine_cluster_seqs | 0.033 | 0.004 | 0.037 | |
fine_clustering | 2.308 | 0.024 | 2.347 | |
generate_pseudobulk | 0.188 | 0.000 | 0.189 | |
guess_celltype | 0.041 | 0.004 | 0.045 | |
hushWarning | 0 | 0 | 0 | |
left_join_warn | 0.013 | 0.006 | 0.019 | |
map_axis_labels | 0.267 | 0.012 | 0.284 | |
mutate_cdb | 0.126 | 0.008 | 0.134 | |
pairing_tables | 0.669 | 0.020 | 0.690 | |
plot_cluster_factors | 5.574 | 0.095 | 5.787 | |
purity | 0 | 0 | 0 | |
rank_prevalence_ccdb | 0.420 | 1.129 | 2.320 | |
rbind-ContigCellDB-method | 0.150 | 0.001 | 0.165 | |
split_cdb | 0.068 | 0.000 | 0.068 | |
sub-sub-ContigCellDB-character-missing-method | 0.049 | 0.000 | 0.049 | |