| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the ISAnalytics package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ISAnalytics.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 944/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ISAnalytics 1.2.1 (landing page) Andrea Calabria
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ISAnalytics |
| Version: 1.2.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISAnalytics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ISAnalytics_1.2.1.tar.gz |
| StartedAt: 2021-10-15 00:53:29 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:15:11 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 1301.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ISAnalytics.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISAnalytics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ISAnalytics_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ISAnalytics.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ISAnalytics/DESCRIPTION' ... OK
* this is package 'ISAnalytics' version '1.2.1'
* 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 'ISAnalytics' 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
* 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CIS_grubbs 4.25 0.21 16.25
CIS_volcano_plot 4.22 0.13 14.39
sample_statistics 2.34 0.12 12.41
realign_after_collisions 1.58 0.27 20.32
HSC_population_plot 1.55 0.08 20.77
remove_collisions 1.52 0.11 19.61
HSC_population_size_estimate 1.47 0.08 18.75
separate_quant_matrices 1.23 0.16 10.75
import_parallel_Vispa2Matrices_auto 1.14 0.11 13.74
compute_near_integrations 1.05 0.18 16.75
cumulative_count_union 1.17 0.04 10.78
comparison_matrix 0.94 0.11 20.97
aggregate_values_by_key 0.94 0.03 11.06
import_Vispa2_stats 0.81 0.12 8.26
import_single_Vispa2Matrix 0.72 0.08 8.78
compute_abundance 0.73 0.06 7.88
as_sparse_matrix 0.51 0.18 8.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CIS_grubbs 5.38 0.19 15.74
CIS_volcano_plot 4.44 0.09 14.90
sample_statistics 2.47 0.22 12.53
realign_after_collisions 1.86 0.11 20.88
remove_collisions 1.80 0.09 21.69
HSC_population_size_estimate 1.62 0.09 19.18
HSC_population_plot 1.50 0.07 19.94
compute_near_integrations 1.28 0.09 15.61
separate_quant_matrices 1.22 0.05 10.84
aggregate_values_by_key 1.20 0.06 11.28
cumulative_count_union 1.14 0.11 11.47
comparison_matrix 1.08 0.13 11.14
import_parallel_Vispa2Matrices_auto 1.11 0.03 11.65
import_Vispa2_stats 0.78 0.06 8.15
as_sparse_matrix 0.70 0.09 7.43
compute_abundance 0.70 0.05 8.23
import_single_Vispa2Matrix 0.64 0.08 7.90
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
== Failed tests ================================================================
-- Error (test-import-im-single.R:155:5): import_single_Vispa2Matrix reads type NEW different params --
Error: Cannot open file for writing:
* 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp0SHftc\filee68363848ca.tsv'
Backtrace:
x
1. \-readr::write_tsv(...) test-import-im-single.R:155:4
2. \-readr::write_delim(...)
3. \-vroom::vroom_write(...)
4. \-vroom:::vroom_write_(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 810 ]
Error: Test failures
Execution halted
** running tests for arch 'x64' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
== Failed tests ================================================================
-- Error (test-import-im-single.R:155:5): import_single_Vispa2Matrix reads type NEW different params --
Error: Cannot open file for writing:
* 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4ExIrF\file2278176d1ab8.tsv'
Backtrace:
x
1. \-readr::write_tsv(...) test-import-im-single.R:155:4
2. \-readr::write_delim(...)
3. \-vroom::vroom_write(...)
4. \-vroom:::vroom_write_(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 810 ]
Error: Test failures
Execution halted
* 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 ERRORs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/ISAnalytics.Rcheck/00check.log'
for details.
ISAnalytics.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ISAnalytics_1.2.1.tar.gz && rm -rf ISAnalytics.buildbin-libdir && mkdir ISAnalytics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ISAnalytics.buildbin-libdir ISAnalytics_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ISAnalytics_1.2.1.zip && rm ISAnalytics_1.2.1.tar.gz ISAnalytics_1.2.1.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
83 1906k 83 1592k 0 0 1903k 0 0:00:01 --:--:-- 0:00:01 1902k
100 1906k 100 1906k 0 0 2074k 0 --:--:-- --:--:-- --:--:-- 2074k
install for i386
* installing *source* package 'ISAnalytics' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ISAnalytics'
finding HTML links ... done
CIS_grubbs html
CIS_volcano_plot html
HSC_population_plot html
HSC_population_size_estimate html
ISAnalytics html
aggregate_metadata html
aggregate_values_by_key html
annotation_IS_vars html
as_sparse_matrix html
association_file_columns html
available_outlier_tests html
blood_lineages_default html
clinical_relevant_suspicious_genes html
comparison_matrix html
compute_abundance html
compute_near_integrations html
cumulative_count_union html
date_columns_coll html
date_formats html
default_iss_file_prefixes html
default_meta_agg html
default_stats html
generate_Vispa2_launch_AF html
generate_blank_association_file html
import_Vispa2_stats html
import_association_file html
import_parallel_Vispa2Matrices_auto html
import_parallel_Vispa2Matrices_interactive
html
import_single_Vispa2Matrix html
known_clinical_oncogenes html
mandatory_IS_vars html
matching_options html
outlier_filter html
outliers_by_pool_fragments html
quantification_types html
realign_after_collisions html
reduced_AF_columns html
remove_collisions html
sample_statistics html
separate_quant_matrices html
threshold_filter html
top_integrations html
unzip_file_system html
*** 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
install for x64
* installing *source* package 'ISAnalytics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ISAnalytics' as ISAnalytics_1.2.1.zip
* DONE (ISAnalytics)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ISAnalytics' successfully unpacked and MD5 sums checked
|
ISAnalytics.Rcheck/tests_i386/testthat.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(ISAnalytics)
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
>
> test_check("ISAnalytics")
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Identifying collisions...
Processing collisions...
Finished! You provided a single sequence count as matrix, to re-align other related matrices see ?realign_after_collisions
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: skipped
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: no problems detected
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: problems detected
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: skipped
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: no problems detected
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: no problems detected
Duplicates found for some files
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Some files are missing and will be ignored
adding: Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp0SHftc/filee681f323ef3.tsv (deflated 43%)
|
| | 0%
|
|======================================================================| 100%
Calculating number of IS for each group...
|
| | 0%
|
|======================================================================| 100%
== Failed tests ================================================================
-- Error (test-import-im-single.R:155:5): import_single_Vispa2Matrix reads type NEW different params --
Error: Cannot open file for writing:
* 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp0SHftc\filee68363848ca.tsv'
Backtrace:
x
1. \-readr::write_tsv(...) test-import-im-single.R:155:4
2. \-readr::write_delim(...)
3. \-vroom::vroom_write(...)
4. \-vroom:::vroom_write_(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 810 ]
Error: Test failures
Execution halted
|
ISAnalytics.Rcheck/tests_x64/testthat.Rout.fail
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(ISAnalytics)
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
>
> test_check("ISAnalytics")
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
|
| | 0%
|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
|
|======================================================================| 100%
Identifying collisions...
Processing collisions...
Finished! You provided a single sequence count as matrix, to re-align other related matrices see ?realign_after_collisions
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: skipped
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: no problems detected
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: problems detected
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: skipped
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: no problems detected
*** Association file import summary ***
i For detailed report please set option 'ISAnalytics.widgets' to TRUE
* Parsing problems detected: TRUE
* Date parsing problems: TRUE
* Column problems detected: TRUE
* NAs found in important columns: TRUE
* File system alignment: no problems detected
Duplicates found for some files
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Some files are missing and will be ignored
adding: Users/biocbuild/bbs-3.13-bioc/tmpdir/Rtmp4ExIrF/file22781f7875.tsv (deflated 43%)
|
| | 0%
|
|======================================================================| 100%
Calculating number of IS for each group...
|
| | 0%
|
|======================================================================| 100%
== Failed tests ================================================================
-- Error (test-import-im-single.R:155:5): import_single_Vispa2Matrix reads type NEW different params --
Error: Cannot open file for writing:
* 'C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmp4ExIrF\file2278176d1ab8.tsv'
Backtrace:
x
1. \-readr::write_tsv(...) test-import-im-single.R:155:4
2. \-readr::write_delim(...)
3. \-vroom::vroom_write(...)
4. \-vroom:::vroom_write_(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 810 ]
Error: Test failures
Execution halted
|
|
ISAnalytics.Rcheck/examples_i386/ISAnalytics-Ex.timings
|
ISAnalytics.Rcheck/examples_x64/ISAnalytics-Ex.timings
|