Pacome Prompsy
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/ChromSCape |
| git_branch: RELEASE_3_14 |
| git_last_commit: df9f2c5 |
| git_last_commit_date: 2021-10-26 13:03:23 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:20 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 ChromSCape package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChromSCape.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 313/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChromSCape 1.4.0 (landing page) Pacome Prompsy
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ChromSCape |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChromSCape.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChromSCape_1.4.0.tar.gz |
| StartedAt: 2022-04-12 17:16:45 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:46:19 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1774.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChromSCape.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChromSCape.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ChromSCape_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ChromSCape.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChromSCape/DESCRIPTION' ... OK
* this is package 'ChromSCape' version '1.4.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ChromSCape' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.1Mb
sub-directories of 1Mb or more:
data 1.3Mb
libs 2.0Mb
www 2.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
CompareWilcox: no visible binding for global variable 'annot.'
bams_to_matrix_indexes: no visible binding for global variable
'files_dir_list'
filter_correlated_cell_scExp: no visible binding for global variable
'run_tsne'
generate_analysis: no visible binding for global variable 'k'
generate_analysis: no visible binding for global variable
'clusterConsensus'
get_most_variable_cyto: no visible binding for global variable
'cytoBand'
get_most_variable_cyto: no visible binding for global variable
'Fri_cyto'
num_cell_after_QC_filt_scExp: no visible binding for global variable
'sample_id'
num_cell_after_QC_filt_scExp: no visible binding for global variable
'total_counts'
num_cell_scExp: no visible binding for global variable 'sample_id'
num_cell_scExp: no visible binding for global variable 'total_counts'
plot_gain_or_loss_barplots: no visible binding for global variable
'Gain_or_Loss'
plot_gain_or_loss_barplots: no visible binding for global variable
'ncells'
plot_gain_or_loss_barplots: no visible binding for global variable
'cytoBand'
plot_most_contributing_features: no visible binding for global variable
'genes'
plot_pie_most_contributing_chr: no visible binding for global variable
'absolute_value'
plot_reduced_dim_scExp: no visible binding for global variable 'V1'
plot_reduced_dim_scExp: no visible binding for global variable 'V2'
plot_reduced_dim_scExp: no visible binding for global variable
'cluster'
subset_bam_call_peaks: no visible binding for global variable
'merged_bam'
Undefined global functions or variables:
Fri_cyto Gain_or_Loss V1 V2 absolute_value annot. cluster
clusterConsensus cytoBand files_dir_list genes k merged_bam ncells
run_tsne sample_id total_counts
* checking Rd files ... NOTE
prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
* 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/ChromSCape/libs/i386/ChromSCape.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/ChromSCape/libs/x64/ChromSCape.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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' ... NOTE
Files named as vignettes but with no recognized vignette engine:
'vignettes/PairedTag_Zhu_H3K4me1.Rmd'
'vignettes/scChIC_Ku_H3K4me3.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_gain_or_loss_barplots 51.97 0.01 51.98
calculate_cyto_mat 27.30 0.11 27.41
calculate_logRatio_CNA 26.12 0.17 26.30
plot_reduced_dim_scExp_CNA 25.45 0.01 25.47
calculate_CNA 25.02 0.39 25.40
calculate_gain_or_loss 25.25 0.08 25.33
get_most_variable_cyto 25.02 0.05 25.06
get_cyto_features 21.78 0.00 21.78
CompareedgeRGLM 15.94 0.57 16.52
num_cell_after_cor_filt_scExp 10.71 0.08 26.25
filter_correlated_cell_scExp 9.72 0.11 25.29
create_scDataset_raw 7.56 0.71 8.28
import_scExp 7.84 0.04 7.89
plot_reduced_dim_scExp 6.49 0.00 6.49
differential_analysis_scExp 4.67 0.21 129.09
CompareWilcox 4.36 0.46 63.10
peaks_to_bins 3.28 0.12 6.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_gain_or_loss_barplots 54.14 0.03 54.17
calculate_CNA 29.84 0.55 30.39
plot_reduced_dim_scExp_CNA 26.53 0.03 26.57
calculate_cyto_mat 26.42 0.07 26.50
calculate_logRatio_CNA 25.79 0.11 25.89
get_most_variable_cyto 25.34 0.03 25.37
calculate_gain_or_loss 24.62 0.11 24.74
get_cyto_features 22.07 0.00 22.07
CompareedgeRGLM 13.33 0.36 13.68
filter_correlated_cell_scExp 12.50 0.08 30.69
num_cell_after_cor_filt_scExp 12.16 0.08 30.36
import_scExp 8.29 0.01 8.31
create_scDataset_raw 7.64 0.56 8.22
differential_analysis_scExp 4.97 0.22 132.87
CompareWilcox 4.63 0.24 73.61
peaks_to_bins 3.36 0.09 6.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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: 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.
ChromSCape.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ChromSCape_1.4.0.tar.gz && rm -rf ChromSCape.buildbin-libdir && mkdir ChromSCape.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChromSCape.buildbin-libdir ChromSCape_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ChromSCape_1.4.0.zip && rm ChromSCape_1.4.0.tar.gz ChromSCape_1.4.0.zip
###
##############################################################################
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 13.5M 0 2486 0 0 30197 0 0:07:50 --:--:-- 0:07:50 30317
25 13.5M 25 3530k 0 0 3282k 0 0:00:04 0:00:01 0:00:03 3284k
60 13.5M 60 8463k 0 0 4079k 0 0:00:03 0:00:02 0:00:01 4078k
89 13.5M 89 12.1M 0 0 4035k 0 0:00:03 0:00:03 --:--:-- 4035k
100 13.5M 100 13.5M 0 0 3981k 0 0:00:03 0:00:03 --:--:-- 3981k
install for i386
* installing *source* package 'ChromSCape' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c as_dist.cpp -o as_dist.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ChromSCape.buildbin-libdir/00LOCK-ChromSCape/00new/ChromSCape/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ChromSCape'
finding HTML links ... done
CompareWilcox html
CompareedgeRGLM html
DA_custom html
DA_one_vs_rest_fun html
DA_pairwise html
H1proportion html
annotToCol2 html
annotation_from_merged_peaks html
anocol_binary html
anocol_categorical html
bams_to_matrix_indexes html
beds_to_matrix_indexes html
calculate_CNA html
calculate_cyto_mat html
calculate_gain_or_loss html
calculate_logRatio_CNA html
call_macs2_merge_peaks html
changeRange html
check_correct_datamatrix html
choose_cluster_scExp html
choose_perplexity html
col2hex html
colors_scExp html
combine_datamatrix html
combine_enrichmentTests html
concatenate_scBed_into_clusters html
consensus_clustering_scExp html
correlation_and_hierarchical_clust_scExp
html
count_coverage html
create_project_folder html
create_sample_name_mat html
create_scDataset_raw html
create_scExp html
define_feature html
detect_samples html
differential_analysis_scExp html
distPearson html
enrichmentTest html
exclude_features_scExp html
feature_annotation_scExp html
filter_correlated_cell_scExp html
filter_genes_with_refined_peak_annotation
html
filter_scExp html
find_top_features html
gene_set_enrichment_analysis_scExp html
generate_analysis html
generate_count_matrix html
generate_coverage_tracks html
generate_feature_names html
getExperimentNames html
getMainExperiment html
get_color_dataframe_from_input html
get_cyto_features html
get_genomic_coordinates html
get_most_variable_cyto html
gg_fill_hue html
groupMat html
has_genomic_coordinates html
hclustAnnotHeatmapPlot html
hg38.GeneTSS html
hg38.chromosomes html
hg38.cytoBand html
imageCol html
import_count_input_files html
import_scExp html
index_peaks_barcodes_to_matrix_indexes
html
inter_correlation_scExp html
intra_correlation_scExp html
launchApp html
load_MSIGdb html
merge_MACS2_peaks html
mm10.GeneTSS html
mm10.chromosomes html
mm10.cytoBand html
normalize_scExp html
num_cell_after_QC_filt_scExp html
num_cell_after_cor_filt_scExp html
num_cell_before_cor_filt_scExp html
num_cell_in_cluster_scExp html
num_cell_scExp html
pca_irlba_for_sparseMatrix html
peaks_to_bins html
plot_cluster_consensus_scExp html
plot_coverage_BigWig html
plot_differential_H1_scExp html
plot_differential_summary_scExp html
plot_differential_volcano_scExp html
plot_distribution_scExp html
plot_gain_or_loss_barplots html
plot_heatmap_scExp html
plot_inter_correlation_scExp html
plot_intra_correlation_scExp html
plot_most_contributing_features html
plot_pie_most_contributing_chr html
plot_reduced_dim_scExp html
plot_reduced_dim_scExp_CNA html
preprocess_CPM html
preprocess_RPKM html
preprocess_TFIDF html
preprocess_TPM html
preprocess_feature_size_only html
raw_counts_to_sparse_matrix html
rawfile_ToBigWig html
read_count_mat_with_separated_chr_start_end
html
read_sparse_matrix html
reduce_dim_batch_correction html
reduce_dims_scExp html
remove_chr_M_fun html
remove_non_canonical_fun html
results_enrichmentTest html
retrieve_top_bot_features_pca html
run_pairwise_tests html
run_tsne_scExp html
scExp html
separate_BAM_into_clusters html
separator_count_mat html
smoothBin html
subsample_scExp html
subset_bam_call_peaks html
swapAltExp_sameColData html
table_enriched_genes_scExp html
warning_DA html
warning_filter_correlated_cell_scExp html
warning_plot_reduced_dim_scExp html
warning_raw_counts_to_sparse_matrix html
wrapper_Signac_FeatureMatrix html
** 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
install for x64
* installing *source* package 'ChromSCape' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c as_dist.cpp -o as_dist.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ChromSCape.buildbin-libdir/ChromSCape/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChromSCape' as ChromSCape_1.4.0.zip
* DONE (ChromSCape)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ChromSCape' successfully unpacked and MD5 sums checked
|
ChromSCape.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(ChromSCape)
>
> test_check("ChromSCape")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
40.01 3.07 73.26
|
ChromSCape.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(ChromSCape)
>
> test_check("ChromSCape")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
45.35 1.18 81.14
|
|
ChromSCape.Rcheck/examples_i386/ChromSCape-Ex.timings
|
ChromSCape.Rcheck/examples_x64/ChromSCape-Ex.timings
|