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This page was generated on 2022-01-14 13:06:15 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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

CHECK results for dasper on tokay2


To the developers/maintainers of the dasper package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dasper.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.

raw results

Package 452/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dasper 1.4.1  (landing page)
David Zhang
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/dasper
git_branch: RELEASE_3_14
git_last_commit: b012447
git_last_commit_date: 2022-01-10 17:32:01 -0500 (Mon, 10 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: dasper
Version: 1.4.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dasper.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dasper_1.4.1.tar.gz
StartedAt: 2022-01-13 17:59:38 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 18:29:18 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 1779.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: dasper.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dasper.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings dasper_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/dasper.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dasper/DESCRIPTION' ... OK
* this is package 'dasper' version '1.4.1'
* 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 'dasper' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/dasper.Rcheck/00install.out' for details.
* 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 ... NOTE
Unexported object imported by a ':::' call: 'grid:::calcControlPoints'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.classify_junc: no visible binding for global variable 'lend'
.classify_junc: no visible binding for global variable 'rstart'
.coverage_to_plot_get: no visible binding for global variable '.'
.coverage_to_plot_get: no visible binding for global variable
  'case_control'
.get_ref_exons_annot: no visible binding for global variable '.'
.plot_coverage: no visible binding for global variable 'case_control'
.plot_junctions: no visible binding for global variable 'size'
annotate_junc_ref: no visible global function definition for
  'ensemblGenome'
annotate_junc_ref: no visible global function definition for
  'basedir<-'
annotate_junc_ref: no visible global function definition for 'read.gtf'
annotate_junc_ref: no visible global function definition for
  'getSpliceTable'
Undefined global functions or variables:
  . basedir<- case_control ensemblGenome getSpliceTable lend read.gtf
  rstart size
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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
coverage_process 141.34  37.62  269.83
junction_process  67.69   1.99   70.45
plot_sashimi      37.72   1.36   39.61
ref_load          14.40   1.53   16.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
coverage_process 126.36  20.50  160.41
junction_process  62.91   1.15   64.58
plot_sashimi      38.04   0.86   39.39
ref_load          14.05   0.38   14.90
* 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:
    1. +-`%>%`(...)
    2. +-base::unlist(.)
    3. +-BiocGenerics::lapply(., FUN = mean)
    4. +-dasper:::.coverage_load(...)
    5. | +-rtracklayer::import(coverage_path, which = regions, as = "NumericList")
    6. | \-rtracklayer::import(coverage_path, which = regions, as = "NumericList")
    7. |   +-BiocIO::import(FileForFormat(con), ...)
    8. |   \-rtracklayer::import(FileForFormat(con), ...)
    9. |     \-rtracklayer:::.local(con, format, text, ...)
   10. \-base::.handleSimpleError(...)
   11.   \-base:::h(simpleError(msg, call))
  
  [ FAIL 3 | WARN 3 | SKIP 1 | PASS 176 ]
  Error: Test failures
  Execution halted
** 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: 1 ERROR, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/dasper.Rcheck/00check.log'
for details.


Installation output

dasper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/dasper_1.4.1.tar.gz && rm -rf dasper.buildbin-libdir && mkdir dasper.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dasper.buildbin-libdir dasper_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL dasper_1.4.1.zip && rm dasper_1.4.1.tar.gz dasper_1.4.1.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
 31 1023k   31  326k    0     0  1791k      0 --:--:-- --:--:-- --:--:-- 1795k
100 1023k  100 1023k    0     0  4274k      0 --:--:-- --:--:-- --:--:-- 4265k

install for i386

* installing *source* package 'dasper' ...
** using non-staged installation via StagedInstall field
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dasper'
    finding HTML links ... done
    coverage_process                        html  
    dasper                                  html  
    deprecated                              html  
    junction_load                           html  
    junction_process                        html  
    junctions_example                       html  
    finding level-2 HTML links ... done

    outlier_process                         html  
    plot_sashimi                            html  
    ref_load                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'dasper' ...
** using non-staged installation via StagedInstall field
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dasper' as dasper_1.4.1.zip
* DONE (dasper)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'dasper' successfully unpacked and MD5 sums checked

Tests output

dasper.Rcheck/tests_i386/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(dasper)
> 
> test_check("dasper")
Starting 2 test processes
== Skipped tests ===============================================================
* On CRAN (1)

== Failed tests ================================================================
-- Error (test-outlier_process.R:42:1): (code run outside of `test_that()`) ----
<bplist_error/bperror/error/condition>
Error: BiocParallel errors
  1 remote errors, element index: 1
  1 unevaluated and other errors
  first remote error: Your current architecture is 32bit; however, this version of Python was compiled for 64bit.
Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment.
Backtrace:
    x
 1. +-dasper::outlier_detect(...)
 2. | +-`%>%`(...)
 3. | +-BiocParallel::bplapply(...)
 4. | \-BiocParallel::bplapply(...)
 5. +-base::matrix(., nrow = dim(junctions)[1], ncol = dim(junctions)[2])
 6. \-base::unlist(.)
-- Error (test-plot_sashimi.R:343:1): (code run outside of `test_that()`) ------
Error in `.local(con, format, text, ...)`: UCSC library operation failed
Backtrace:
     x
  1. +-dasper:::.coverage_to_plot_get(...)
  2. | +-`%>%`(...)
  3. | \-dasper:::.coverage_load(...)
  4. |   +-rtracklayer::import(coverage_path, which = regions, as = "NumericList")
  5. |   \-rtracklayer::import(coverage_path, which = regions, as = "NumericList")
  6. |     +-BiocIO::import(FileForFormat(con), ...)
  7. |     \-rtracklayer::import(FileForFormat(con), ...)
  8. |       \-rtracklayer:::.local(con, format, text, ...)
  9. +-dplyr::mutate(., case_control = "case")
 10. +-dplyr::tibble(...)
 11. | \-tibble:::tibble_quos(xs, .rows, .name_repair)
 12. |   \-rlang::eval_tidy(xs[[j]], mask)
 13. \-base::unlist(.)
-- Error (test-utils.R:53:1): (code run outside of `test_that()`) --------------
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'X' in selecting a method for function 'lapply': UCSC library operation failed
Backtrace:
     x
  1. +-`%>%`(...)
  2. +-base::unlist(.)
  3. +-BiocGenerics::lapply(., FUN = mean)
  4. +-dasper:::.coverage_load(...)
  5. | +-rtracklayer::import(coverage_path, which = regions, as = "NumericList")
  6. | \-rtracklayer::import(coverage_path, which = regions, as = "NumericList")
  7. |   +-BiocIO::import(FileForFormat(con), ...)
  8. |   \-rtracklayer::import(FileForFormat(con), ...)
  9. |     \-rtracklayer:::.local(con, format, text, ...)
 10. \-base::.handleSimpleError(...)
 11.   \-base:::h(simpleError(msg, call))

[ FAIL 3 | WARN 3 | SKIP 1 | PASS 176 ]
Error: Test failures
Execution halted

dasper.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(dasper)
> 
> test_check("dasper")
Starting 2 test processes
== Skipped tests ===============================================================
* On CRAN (3)

[ FAIL 0 | WARN 1 | SKIP 3 | PASS 228 ]
> 
> proc.time()
   user  system elapsed 
   8.29    0.79  434.32 

Example timings

dasper.Rcheck/examples_i386/dasper-Ex.timings

nameusersystemelapsed
coverage_process141.34 37.62269.83
junction_load0.220.000.30
junction_process67.69 1.9970.45
outlier_process000
plot_sashimi37.72 1.3639.61
ref_load14.40 1.5316.44

dasper.Rcheck/examples_x64/dasper-Ex.timings

nameusersystemelapsed
coverage_process126.36 20.50160.41
junction_load0.240.040.25
junction_process62.91 1.1564.58
outlier_process000
plot_sashimi38.04 0.8639.39
ref_load14.05 0.3814.90