Back to Long Tests report for BioC 3.21

This page was generated on 2025-03-22 23:55 -0400 (Sat, 22 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4547
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
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 15/30HostnameOS / ArchCHECK
crisprScore 1.11.0  (landing page)
Jean-Philippe Fortin
Snapshot Date: 2025-03-22 09:55 -0400 (Sat, 22 Mar 2025)
git_url: https://git.bioconductor.org/packages/crisprScore
git_branch: devel
git_last_commit: d409224
git_last_commit_date: 2024-10-29 11:07:33 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for crisprScore on palomino7

To the developers/maintainers of the crisprScore 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: crisprScore
Version: 1.11.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.11.0.tar.gz
StartedAt: 2025-03-22 16:09:05 -0400 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 16:33:32 -0400 (Sat, 22 Mar 2025)
EllapsedTime: 1466.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: crisprScore.Rcheck
Warnings: NA

Tests output

crisprScore.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(crisprScore)
Loading required package: crisprScoreData
Loading required package: ExperimentHub
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> 
> test_check("crisprScore")
Channels:
 - bioconda
 - conda-forge
Platform: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides vc 9.* needed by python-2.7.12-0

Could not solve for environment specs
The following packages are incompatible
\u2514\u2500 python 2.7**  is not installable because there are no viable options
   \u251c\u2500 python [2.7.12|2.7.13|2.7.14|2.7.15] would require
   \u2502  \u2514\u2500 vc 9.* , which does not exist (perhaps a missing channel);
   \u2514\u2500 python 2.7.15 would require
      \u2514\u2500 vc >=9,<10.0a0 , which does not exist (perhaps a missing channel).

Channels:
 - conda-forge
 - bioconda
Platform: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: C:\Users\biocbuild\.basilisk\1.19.3\crisprScore\1.11.0\lindel_basilisk

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pip-21.3.1                 |     pyhd8ed1ab_0         1.2 MB  conda-forge
    python-3.6.15              |h39d44d4_0_cpython        18.9 MB  conda-forge
    python_abi-3.6             |          2_cp36m           4 KB  conda-forge
    setuptools-58.0.4          |   py36ha15d459_2         959 KB  conda-forge
    wheel-0.37.1               |     pyhd8ed1ab_0          31 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        21.1 MB

The following NEW packages will be INSTALLED:

  pip                conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0 
  python             conda-forge/win-64::python-3.6.15-h39d44d4_0_cpython 
  python_abi         conda-forge/win-64::python_abi-3.6-2_cp36m 
  setuptools         conda-forge/win-64::setuptools-58.0.4-py36ha15d459_2 
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_1 
  vc                 conda-forge/win-64::vc-14.3-hbf610ac_24 
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.42.34438-hfd919c2_24 
  vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.42.34438-h7142326_24 
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - bioconda
Platform: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.1.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - conda-forge
 - bioconda
Platform: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.1.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



## Package Plan ##

  environment location: C:\Users\biocbuild\.basilisk\1.19.3\crisprScore\1.11.0\lindel_basilisk

  added / updated specs:
    - numpy=1.19.5
    - pip=21.0.1
    - python[version='3.6.*,3.6.*']
    - scipy=1.5.3


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    numpy-1.19.5               |   py36h4b40d73_2         4.9 MB  conda-forge
    pip-21.0.1                 |     pyhd8ed1ab_0         1.1 MB  conda-forge
    scipy-1.5.3                |   py36h27d303f_1        21.9 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        27.8 MB

The following NEW packages will be INSTALLED:

  intel-openmp       conda-forge/win-64::intel-openmp-2024.2.1-h57928b3_1083 
  libblas            conda-forge/win-64::libblas-3.9.0-31_h641d27c_mkl 
  libcblas           conda-forge/win-64::libcblas-3.9.0-31_h5e41251_mkl 
  libhwloc           conda-forge/win-64::libhwloc-2.11.2-default_hc8275d1_1000 
  libiconv           conda-forge/win-64::libiconv-1.18-h135ad9c_1 
  liblapack          conda-forge/win-64::liblapack-3.9.0-31_h1aa476e_mkl 
  libxml2            conda-forge/win-64::libxml2-2.13.6-he286e8c_0 
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_2 
  m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6 
  m2w64-gcc-libs     conda-forge/win-64::m2w64-gcc-libs-5.3.0-7 
  m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7 
  m2w64-gmp          conda-forge/win-64::m2w64-gmp-6.1.0-2 
  m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2 
  mkl                conda-forge/win-64::mkl-2024.2.2-h66d3029_15 
  msys2-conda-epoch  conda-forge/win-64::msys2-conda-epoch-20160418-1 
  numpy              conda-forge/win-64::numpy-1.19.5-py36h4b40d73_2 
  pthreads-win32     conda-forge/win-64::pthreads-win32-2.9.1-h2466b09_4 
  scipy              conda-forge/win-64::scipy-1.5.3-py36h27d303f_1 
  tbb                conda-forge/win-64::tbb-2021.13.0-h62715c5_1 

The following packages will be DOWNGRADED:

  pip                                   21.3.1-pyhd8ed1ab_0 --> 21.0.1-pyhd8ed1ab_0 



Downloading and Extracting Packages: ...working...
scipy-1.5.3          | 21.9 MB   |            |   0% 

numpy-1.19.5         | 4.9 MB    |            |   0% 


pip-21.0.1           | 1.1 MB    |            |   0% 


pip-21.0.1           | 1.1 MB    | 1          |   1% 
scipy-1.5.3          | 21.9 MB   |            |   0% 

numpy-1.19.5         | 4.9 MB    |            |   0% 


pip-21.0.1           | 1.1 MB    | ########## | 100% 
scipy-1.5.3          | 21.9 MB   | ####5      |  46% 

numpy-1.19.5         | 4.9 MB    | ########## | 100% 

numpy-1.19.5         | 4.9 MB    | ########## | 100% 
scipy-1.5.3          | 21.9 MB   | #########8 |  99% 
scipy-1.5.3          | 21.9 MB   | ########## | 100% 


pip-21.0.1           | 1.1 MB    | ########## | 100% 


pip-21.0.1           | 1.1 MB    | ########## | 100% 

numpy-1.19.5         | 4.9 MB    | ########## | 100% 
scipy-1.5.3          | 21.9 MB   | ########## | 100% 
                                                     


                                                     


                                                      done
Preparing transaction: - \ | / done
Verifying transaction: \ | / - \ | / - \ done
Executing transaction: / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
Processing e:\biocbuild\bbs-3.21-bioc-longtests\meat\crisprscore.rcheck\crisprscore\python\lindel
Requirement already satisfied: numpy in c:\users\biocbu~1\basili~1\119~1.3\crispr~1\111~1.0\lindel~1\lib\site-packages (from Lindel==1.0) (1.19.5)
Requirement already satisfied: scipy in c:\users\biocbu~1\basili~1\119~1.3\crispr~1\111~1.0\lindel~1\lib\site-packages (from Lindel==1.0) (1.5.3)
Building wheels for collected packages: Lindel
  Building wheel for Lindel (setup.py): started
  Building wheel for Lindel (setup.py): finished with status 'done'
  Created wheel for Lindel: filename=Lindel-1.0-py3-none-any.whl size=33618 sha256=afbda85bd7590eeb7034596bd567985d08dda5a1e5a57c55cbf7f68598418e9d
  Stored in directory: E:\biocbuild\bbs-3.21-bioc-longtests\tmpdir\pip-ephem-wheel-cache-bz_gducv\wheels\77\5f\94\304b5ea7aa09e70e71bd613f8180b3ca79153e687387bf2472
Successfully built Lindel
Installing collected packages: Lindel
Successfully installed Lindel-1.0
[ FAIL 1 | WARN 4 | SKIP 3 | PASS 1 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On Windows (3): 'test-ontargets.R:23:5', 'test-ontargets.R:28:5',
  'test-ontargets.R:37:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ontargets.R:19:5'): Azimuth scores ─────────────────────────────
Error: Error creating conda environment 'C:/Users/biocbuild/.basilisk/1.19.3/crisprScore/1.11.0/azimuth_basilisk' [exit code 1]
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test-ontargets.R:19:5
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─crisprScore::getAzimuthScores(azimuth_sequences)
 5.   └─basilisk::obtainEnvironmentPath(env_azimuth)
 6.     └─basilisk::setupBasiliskEnv(...)
 7.       └─reticulate::conda_install(...)
 8.         └─reticulate::conda_create(...)
 9.           └─reticulate:::stopf(fmt, envname, result, call. = FALSE)

[ FAIL 1 | WARN 4 | SKIP 3 | PASS 1 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no crisprScore_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'crisprScore/DESCRIPTION' ... OK
* this is package 'crisprScore' version '1.11.0'
* 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 ... NOTE
Found the following non-portable file paths:
  crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.data-00000-of-00001
  crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.index
  crisprScore/inst/python/deepspcas9/DeepCas9_Final/PreTrain-Final-False-3-5-7-100-70-40-0.001-550-True-80-60.meta

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'crisprScore' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck/00install.out' for details.
* checking installed package size ... INFO
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    python   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': 'basilisk.utils:::getPythonBinary'
  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 ... 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 ... SKIPPED
* 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 R/sysdata.rda ... OK
* checking line endings in shell scripts ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-ontargets.R:19:5
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─crisprScore::getAzimuthScores(azimuth_sequences)
   5.   └─basilisk::obtainEnvironmentPath(env_azimuth)
   6.     └─basilisk::setupBasiliskEnv(...)
   7.       └─reticulate::conda_install(...)
   8.         └─reticulate::conda_create(...)
   9.           └─reticulate:::stopf(fmt, envname, result, call. = FALSE)
  
  [ FAIL 1 | WARN 4 | SKIP 3 | PASS 1 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 4 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc-longtests/meat/crisprScore.Rcheck/00check.log'
for details.

Installation output

crisprScore.Rcheck/00install.out

* installing *source* package 'crisprScore' ...
** this is package 'crisprScore' version '1.11.0'
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (crisprScore)