Andrew McDavid
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/CellaRepertorium |
| Branch: RELEASE_3_12 |
| Last Commit: 4e5b113 |
| Last Changed Date: 2020-10-27 12:03:47 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:27:04 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the CellaRepertorium package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 249/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellaRepertorium 1.0.0 (landing page) Andrew McDavid
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CellaRepertorium |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CellaRepertorium_1.0.0.tar.gz |
| StartedAt: 2021-05-05 23:49:24 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 23:51:54 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 150.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CellaRepertorium.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CellaRepertorium.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CellaRepertorium_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CellaRepertorium.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 ... 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
fancy_name_contigs: no visible binding for global variable ‘.’
pairing_tables: no visible binding for global variable ‘.’
Undefined global functions or variables:
.
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cluster_logistic_test 6.26 0.084 6.973
* 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
‘/home/biocbuild/bbs-3.12-bioc/meat/CellaRepertorium.Rcheck/00check.log’
for details.
CellaRepertorium.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CellaRepertorium
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CellaRepertorium’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/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:2:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:494:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:160:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:174:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:2418:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:2435:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:2437:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush (stop)
cdhit-common.cpp:2458:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
cdhit-common.cpp:2467:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
#pragma omp flush (stop)
cdhit-common.cpp:2492:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
cdhit-common.cpp:3151:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for schedule( dynamic, 1 )
In file included from cdhit-common.cpp:37:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:494:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
int max_diag = 0;
^~~~~~~~
cdhit-common.cpp: In member function ‘void SequenceDB::SortDivide(Options&, bool)’:
cdhit-common.cpp:1774:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (len > max_len) max_len = len;
~~~~^~~~~~~~~
cdhit-common.cpp:1775:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
size_t mem, mega = 1000000;
^~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/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:32:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:494:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:0:
cdhit-common.h: In member function ‘void WorkingBuffer::Set(size_t, size_t, const Options&)’:
cdhit-common.h:494:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( band > options.band_width ) band = options.band_width;
~~~~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c progress.cpp -o progress.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 1 | SKIP 0 | PASS 73 ]
>
> proc.time()
user system elapsed
24.072 0.712 24.825
CellaRepertorium.Rcheck/CellaRepertorium-Ex.timings
| name | user | system | elapsed | |
| ContigCellDB-fun | 0.296 | 0.020 | 0.316 | |
| canonicalize_cell | 0.304 | 0.036 | 0.337 | |
| canonicalize_cluster | 4.172 | 0.060 | 4.241 | |
| cash-ContigCellDB-method | 0.248 | 0.060 | 0.307 | |
| ccdb_join | 0.080 | 0.036 | 0.117 | |
| cdhit | 0.264 | 0.132 | 0.410 | |
| cdhit_ccdb | 0.164 | 0.060 | 0.225 | |
| cluster_filterset | 0.000 | 0.000 | 0.001 | |
| cluster_germline | 0.136 | 0.028 | 0.164 | |
| cluster_logistic_test | 6.260 | 0.084 | 6.973 | |
| cluster_permute_test | 0.724 | 0.008 | 0.734 | |
| cluster_plot | 2.924 | 0.056 | 2.986 | |
| crosstab_by_celltype | 0.104 | 0.016 | 0.121 | |
| entropy | 0.000 | 0.000 | 0.002 | |
| enumerate_pairing | 0.352 | 0.020 | 0.372 | |
| equalize_ccdb | 0.116 | 0.000 | 0.124 | |
| fancy_name_contigs | 0.252 | 0.012 | 0.264 | |
| fine_cluster_seqs | 0.052 | 0.000 | 0.050 | |
| fine_clustering | 2.104 | 0.060 | 2.167 | |
| generate_pseudobulk | 0.160 | 0.032 | 0.190 | |
| guess_celltype | 0.048 | 0.024 | 0.071 | |
| hushWarning | 0.000 | 0.000 | 0.001 | |
| left_join_warn | 0.012 | 0.004 | 0.018 | |
| map_axis_labels | 0.140 | 0.000 | 0.143 | |
| mutate_cdb | 0.116 | 0.068 | 0.183 | |
| pairing_tables | 0.616 | 0.000 | 0.618 | |
| purity | 0.000 | 0.000 | 0.001 | |
| rank_prevalence_ccdb | 0.576 | 0.040 | 0.618 | |
| rbind-ContigCellDB-method | 0.196 | 0.040 | 0.238 | |
| split_cdb | 0.072 | 0.036 | 0.108 | |
| sub-sub-ContigCellDB-character-missing-method | 0.068 | 0.020 | 0.084 | |