| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:37 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: CellaRepertorium |
| Version: 1.12.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CellaRepertorium.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings CellaRepertorium_1.12.0.tar.gz |
| StartedAt: 2024-04-15 23:06:18 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 23:09:34 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 196.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CellaRepertorium.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CellaRepertorium.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings CellaRepertorium_1.12.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/CellaRepertorium.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'CellaRepertorium' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* 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 ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/CellaRepertorium/libs/x64/CellaRepertorium.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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
* 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: 2 NOTEs
See
'F:/biocbuild/bbs-3.18-bioc/meat/CellaRepertorium.Rcheck/00check.log'
for details.
CellaRepertorium.Rcheck/00install.out
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### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL CellaRepertorium
###
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'CellaRepertorium' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:494:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:494:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long 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:545:13: 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:669:13: 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:1774:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
1774 | if (len > max_len) max_len = len;
| ~~~~^~~~~~~~~
cdhit-common.cpp:1775:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long 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:2379:16: warning: variable 'mem' set but not used [-Wunused-but-set-variable]
2379 | size_t mem, mega = 1000000;
| ^~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:494:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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:494:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
494 | if( band > options.band_width ) band = options.band_width;
| ~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c progress.cpp -o progress.o
g++ -std=gnu++17 -shared -s -static-libgcc -o CellaRepertorium.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-CellaRepertorium/00new/CellaRepertorium/libs/x64
** 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
** 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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
23.09 2.10 25.73
CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings
| name | user | system | elapsed | |
| ContigCellDB-fun | 0.21 | 0.28 | 0.50 | |
| canonicalize_cell | 0.36 | 0.14 | 0.50 | |
| canonicalize_cluster | 3.21 | 0.25 | 3.45 | |
| cash-ContigCellDB-method | 0.25 | 0.39 | 0.64 | |
| ccdb_join | 0.09 | 0.16 | 0.25 | |
| cdhit | 0.19 | 0.04 | 0.25 | |
| cdhit_ccdb | 0.19 | 0.13 | 0.33 | |
| cland | 3.50 | 0.25 | 3.76 | |
| cluster_filterset | 0 | 0 | 0 | |
| cluster_germline | 0.12 | 0.16 | 0.28 | |
| cluster_logistic_test | 3.89 | 0.45 | 4.52 | |
| cluster_permute_test | 0.72 | 0.03 | 1.52 | |
| cluster_plot | 2.23 | 0.21 | 2.61 | |
| cross_tab_tbl | 0.16 | 0.01 | 0.17 | |
| crosstab_by_celltype | 0.20 | 0.19 | 0.39 | |
| entropy | 0 | 0 | 0 | |
| enumerate_pairing | 0.66 | 0.19 | 0.86 | |
| equalize_ccdb | 0.09 | 0.00 | 0.09 | |
| fancy_name_contigs | 0.34 | 0.06 | 1.24 | |
| fine_cluster_seqs | 0.03 | 0.02 | 0.04 | |
| fine_clustering | 2.10 | 0.15 | 2.27 | |
| generate_pseudobulk | 0.15 | 0.22 | 0.37 | |
| guess_celltype | 0.05 | 0.25 | 0.30 | |
| hushWarning | 0 | 0 | 0 | |
| left_join_warn | 0.03 | 0.00 | 0.03 | |
| map_axis_labels | 0.21 | 0.00 | 0.24 | |
| mutate_cdb | 0.23 | 0.28 | 0.51 | |
| pairing_tables | 0.37 | 0.00 | 0.38 | |
| plot_cluster_factors | 4.43 | 0.19 | 4.97 | |
| purity | 0 | 0 | 0 | |
| rank_prevalence_ccdb | 0.37 | 0.17 | 0.54 | |
| rbind-ContigCellDB-method | 0.11 | 0.21 | 0.32 | |
| split_cdb | 0.05 | 0.21 | 0.26 | |
| sub-sub-ContigCellDB-character-missing-method | 0.09 | 0.25 | 0.35 | |