Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-06-24 11:07:51 -0400 (Fri, 24 Jun 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" | 4331 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" | 4136 |
lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4147 |
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 FLAMES package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FLAMES.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 662/2118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FLAMES 1.3.3 (landing page) Voogd Oliver
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: FLAMES |
Version: 1.3.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FLAMES_1.3.3.tar.gz |
StartedAt: 2022-06-23 20:13:51 -0400 (Thu, 23 Jun 2022) |
EndedAt: 2022-06-23 20:20:17 -0400 (Thu, 23 Jun 2022) |
EllapsedTime: 386.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FLAMES.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FLAMES.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FLAMES_1.3.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/FLAMES.Rcheck’ * using R version 4.2.0 Patched (2022-05-29 r82424) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FLAMES/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FLAMES’ version ‘1.3.3’ * 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 ‘FLAMES’ 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 generate_sc_sce: no visible binding for global variable 'FSM_match' sc_DTU_analysis: no visible global function definition for 'is' sc_DTU_analysis: no visible binding for global variable 'FSM_match' sc_DTU_analysis: no visible binding for global variable 'gene_name' sc_DTU_analysis: no visible binding for global variable 'cell_id' sc_DTU_analysis: no visible binding for global variable 'cnt' sc_DTU_analysis: no visible binding for global variable 'tr_id' sc_DTU_analysis : get_rm: no visible binding for global variable 'gene_name' sc_DTU_analysis : get_rm: no visible binding for global variable 'l' sc_annotate_umap: no visible binding for global variable 'FSM_match' sc_annotate_umap: no visible binding for global variable 'gene_id' sc_annotate_umap: no visible binding for global variable 'x' sc_annotate_umap: no visible binding for global variable 'y' sc_annotate_umap : plot_idx: no visible binding for global variable 'x' sc_annotate_umap : plot_idx: no visible binding for global variable 'y' sc_annotate_umap : plot_idx_impute: no visible binding for global variable 'x' sc_annotate_umap : plot_idx_impute: no visible binding for global variable 'y' Undefined global functions or variables: FSM_match cell_id cnt gene_id gene_name is l tr_id x y Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/FLAMES/libs/FLAMES.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (C) Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_abort’, possibly from ‘abort’ (C) Found ‘_exit’, possibly from ‘exit’ (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. 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 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/FLAMES.Rcheck/00check.log’ for details.
FLAMES.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FLAMES ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘FLAMES’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppFunctions.cpp -o RcppFunctions.o In file included from RcppFunctions.cpp:7: In file included from ./main-functions/match_cell_barcode.h:16: ./main-functions/../utility/fastq_utils.h:15:1: warning: unused function 'kseq_init' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:165:16: note: expanded from macro '__KSEQ_BASIC' SCOPE kseq_t *kseq_init(type_t fd) \ ^ In file included from RcppFunctions.cpp:7: In file included from ./main-functions/match_cell_barcode.h:16: ./main-functions/../utility/fastq_utils.h:15:1: warning: unused function 'kseq_destroy' [-Wunused-function] /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:171:13: note: expanded from macro '__KSEQ_BASIC' SCOPE void kseq_destroy(kseq_t *ks) \ ^ In file included from RcppFunctions.cpp:7: In file included from ./main-functions/match_cell_barcode.h:16: ./main-functions/../utility/fastq_utils.h:15:1: warning: unused function 'kseq_read' [-Wunused-function] /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:238:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_READ(SCOPE) ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:185:12: note: expanded from macro '__KSEQ_READ' SCOPE int kseq_read(kseq_t *seq) \ ^ 3 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c main-functions/merge_bulk.cpp -o main-functions/merge_bulk.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utility/edit_dist.cpp -o utility/edit_dist.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utility/fastq_utils.cpp -o utility/fastq_utils.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bam.c -o bam.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utility/ssw/ssw.c -o utility/ssw/ssw.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FLAMES.so RcppExports.o RcppFunctions.o main-functions/match_cell_barcode.o main-functions/merge_bulk.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-FLAMES/00new/FLAMES/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (FLAMES)
FLAMES.Rcheck/FLAMES-Ex.timings
name | user | system | elapsed | |
bulk_long_pipeline | 0.494 | 0.128 | 1.027 | |
bulk_windows_pipeline_setup | 0.507 | 0.104 | 0.751 | |
create_config | 0.000 | 0.001 | 0.000 | |
create_sce_from_dir | 0.353 | 0.081 | 0.574 | |
create_se_from_dir | 0.420 | 0.077 | 0.657 | |
get_default_config_file | 0.000 | 0.000 | 0.001 | |
gff3_to_bed12 | 0.001 | 0.001 | 0.001 | |
merge_bulk_fastq | 0.548 | 0.089 | 0.785 | |
merge_bulk_fastq_python | 0.730 | 0.081 | 0.952 | |
parse_gff_tree | 0.546 | 0.024 | 0.649 | |
parse_json_config | 0.001 | 0.000 | 0.001 | |
samtools_as_bam | 1.450 | 0.111 | 1.744 | |
samtools_sort_index | 1.058 | 0.103 | 1.488 | |
sc_long_pipeline | 1.198 | 0.094 | 1.465 | |
sc_windows_pipeline_setup | 0.359 | 0.079 | 0.596 | |
windows_pipeline_isoforms | 0.473 | 0.091 | 0.722 | |
windows_pipeline_quantification | 0.651 | 0.081 | 0.880 | |