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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 1305/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mslp 1.2.0  (landing page)
Chunxuan Shao
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/mslp
git_branch: RELEASE_3_17
git_last_commit: 1d671a5
git_last_commit_date: 2023-04-25 11:38:57 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

CHECK results for mslp on kjohnson2


To the developers/maintainers of the mslp package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: mslp
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mslp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mslp_1.2.0.tar.gz
StartedAt: 2023-10-18 09:40:46 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 09:42:53 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 127.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: mslp.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mslp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mslp_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mslp.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mslp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mslp’ version ‘1.2.0’
* 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 ‘mslp’ 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
est_im    10.372  0.127  17.401
comp_slp   6.085  0.387  11.067
merge_slp  4.932  0.063   7.629
corr_slp   4.472  0.058   8.287
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 ERROR
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  
  test_corr_slp.R...............    0 tests    
  test_corr_slp.R...............    0 tests    
  test_corr_slp.R...............    0 tests    (II) Number of mutations: 5.
  
  test_corr_slp.R...............    0 tests    
  test_corr_slp.R...............    1 tests 1 fails 6.7s
  ----- FAILED[data]: test_corr_slp.R<5--5>
   call| expect_equal(head(res$slp_entrez), c("751071", "10395", "57864", 
   call| -->    "54629", "54898", "1778"))
   diff| 6 string mismatches
  Error: 1 out of 2 tests failed
  In addition: Warning message:
  executing %dopar% sequentially: no parallel backend registered 
  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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/mslp.Rcheck/00check.log’
for details.


Installation output

mslp.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mslp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘mslp’ ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mslp)

Tests output

mslp.Rcheck/tests/tinytest.Rout.fail


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> if (requireNamespace("tinytest", quietly = TRUE)) {
+   tinytest::test_package("mslp")
+ }

test_comp_slp.R...............    0 tests    
test_comp_slp.R...............    0 tests    (==) Number of mutations: 5.


test_comp_slp.R...............    0 tests    
test_comp_slp.R...............    1 tests OK 9.1s

test_corr_slp.R...............    0 tests    
test_corr_slp.R...............    0 tests    
test_corr_slp.R...............    0 tests    (II) Number of mutations: 5.

test_corr_slp.R...............    0 tests    
test_corr_slp.R...............    1 tests 1 fails 6.7s
----- FAILED[data]: test_corr_slp.R<5--5>
 call| expect_equal(head(res$slp_entrez), c("751071", "10395", "57864", 
 call| -->    "54629", "54898", "1778"))
 diff| 6 string mismatches
Error: 1 out of 2 tests failed
In addition: Warning message:
executing %dopar% sequentially: no parallel backend registered 
Execution halted

Example timings

mslp.Rcheck/mslp-Ex.timings

nameusersystemelapsed
comp_slp 6.085 0.38711.067
cons_slp0.0000.0010.000
corr_slp4.4720.0588.287
est_im10.372 0.12717.401
genie30.0160.0010.028
getlink0.0050.0010.012
merge_slp4.9320.0637.629
pp_tcga0.0000.0000.001
scr_slp0.1500.0151.338