Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-07-07 11:11:16 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
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

BUILD results for Herper on kjohnson


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

raw results

Package 877/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Herper 1.7.0  (landing page)
Thomas Carroll
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/Herper
git_branch: master
git_last_commit: 1dbdf55
git_last_commit_date: 2022-04-26 12:09:44 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    TIMEOUT  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.2.1 Monterey / x86_64  OK    TIMEOUT  skippedskipped
kjohnsonmacOS 12.4 Monterey / arm64  OK    ERROR  skippedskipped

Summary

Package: Herper
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Herper
StartedAt: 2022-07-06 22:29:10 -0400 (Wed, 06 Jul 2022)
EndedAt: 2022-07-06 22:31:13 -0400 (Wed, 06 Jul 2022)
EllapsedTime: 122.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Herper
###
##############################################################################
##############################################################################


* checking for file ‘Herper/DESCRIPTION’ ... OK
* preparing ‘Herper’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Herper.Rmd’ using rmarkdown
Loading required package: reticulate
* Installing Miniconda -- please wait a moment ...
* Downloading 'https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh' ...
trying URL 'https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh'
Content type 'application/octet-stream' length 40121896 bytes (38.3 MB)
==================================================
downloaded 38.3 MB

PREFIX=/tmp/RtmpQb4nKx/rr/Test
Unpacking payload ...
Extracting "python_abi-3.9-2_cp39.tar.bz2"
Extracting "idna-3.3-pyhd8ed1ab_0.tar.bz2"
Extracting "six-1.16.0-pyh6c4a22f_0.tar.bz2"
Extracting "tqdm-4.64.0-pyhd8ed1ab_0.tar.bz2"
Extracting "urllib3-1.26.9-pyhd8ed1ab_0.tar.bz2"
Extracting "libzlib-1.2.12-h90dfc92_0.tar.bz2"
Extracting "cryptography-37.0.2-py39h4cb6239_0.tar.bz2"
Extracting "xz-5.2.5-h642e427_1.tar.bz2"
Extracting "wheel-0.37.1-pyhd8ed1ab_0.tar.bz2"
Extracting "conda-4.12.0-py39h2804cbe_0.tar.bz2"
Extracting "python-3.9.13-hc596b02_0_cpython.tar.bz2"
Extracting "pycparser-2.21-pyhd8ed1ab_0.tar.bz2"
Extracting "pip-22.1.2-pyhd8ed1ab_0.tar.bz2"
Extracting "colorama-0.4.4-pyh9f0ad1d_0.tar.bz2"
Extracting "requests-2.27.1-pyhd8ed1ab_0.tar.bz2"
Extracting "pyopenssl-22.0.0-pyhd8ed1ab_0.tar.bz2"
Extracting "brotlipy-0.7.0-py39hb18efdd_1004.tar.bz2"
Extracting "zlib-1.2.12-h90dfc92_0.tar.bz2"
Extracting "pycosat-0.6.3-py39hb18efdd_1010.tar.bz2"
Extracting "ca-certificates-2022.5.18.1-h4653dfc_0.tar.bz2"
Extracting "setuptools-62.3.2-py39h2804cbe_0.tar.bz2"
Extracting "pysocks-1.7.1-py39h2804cbe_5.tar.bz2"
Extracting "tzdata-2022a-h191b570_0.tar.bz2"
Extracting "certifi-2022.5.18.1-py39h2804cbe_0.tar.bz2"
Extracting "readline-8.1-hedafd6a_0.tar.bz2"
Extracting "bzip2-1.0.8-h3422bc3_4.tar.bz2"
Extracting "libffi-3.4.2-h3422bc3_5.tar.bz2"
Extracting "ncurses-6.3-h07bb92c_1.tar.bz2"
Extracting "ruamel_yaml-0.15.80-py39h9eb174b_1007.tar.bz2"
Extracting "cffi-1.15.0-py39h52b1de0_0.tar.bz2"
Extracting "yaml-0.2.5-h3422bc3_2.tar.bz2"
Extracting "tk-8.6.12-he1e0b03_0.tar.bz2"
Extracting "charset-normalizer-2.0.12-pyhd8ed1ab_0.tar.bz2"
Extracting "openssl-1.1.1o-ha287fd2_0.tar.bz2"
Extracting "conda-package-handling-1.8.1-py39hb18efdd_1.tar.bz2"
Extracting "sqlite-3.38.5-h40dfcc0_0.tar.bz2"

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

conda-forge/osx-arm64                                       Using cache
conda-forge/noarch                                          Using cache

Transaction

  Prefix: /private/tmp/RtmpQb4nKx/rr/Test

  Updating specs:

   - python==3.9.13=hc596b02_0_cpython
   - bzip2==1.0.8=h3422bc3_4
   - ca-certificates==2022.5.18.1=h4653dfc_0
   - libffi==3.4.2=h3422bc3_5
   - libzlib==1.2.12=h90dfc92_0
   - ncurses==6.3=h07bb92c_1
   - tzdata==2022a=h191b570_0
   - xz==5.2.5=h642e427_1
   - yaml==0.2.5=h3422bc3_2
   - openssl==1.1.1o=ha287fd2_0
   - readline==8.1=hedafd6a_0
   - tk==8.6.12=he1e0b03_0
   - zlib==1.2.12=h90dfc92_0
   - sqlite==3.38.5=h40dfcc0_0
   - charset-normalizer==2.0.12=pyhd8ed1ab_0
   - colorama==0.4.4=pyh9f0ad1d_0
   - idna==3.3=pyhd8ed1ab_0
   - pycparser==2.21=pyhd8ed1ab_0
   - python_abi==3.9=2_cp39
   - six==1.16.0=pyh6c4a22f_0
   - wheel==0.37.1=pyhd8ed1ab_0
   - certifi==2022.5.18.1=py39h2804cbe_0
   - cffi==1.15.0=py39h52b1de0_0
   - pycosat==0.6.3=py39hb18efdd_1010
   - pysocks==1.7.1=py39h2804cbe_5
   - ruamel_yaml==0.15.80=py39h9eb174b_1007
   - setuptools==62.3.2=py39h2804cbe_0
   - tqdm==4.64.0=pyhd8ed1ab_0
   - brotlipy==0.7.0=py39hb18efdd_1004
   - conda-package-handling==1.8.1=py39hb18efdd_1
   - cryptography==37.0.2=py39h4cb6239_0
   - pip==22.1.2=pyhd8ed1ab_0
   - pyopenssl==22.0.0=pyhd8ed1ab_0
   - urllib3==1.26.9=pyhd8ed1ab_0
   - requests==2.27.1=pyhd8ed1ab_0
   - conda==4.12.0=py39h2804cbe_0


  Package                       Version  Build               Channel                     Size
───────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────

  + brotlipy                      0.7.0  py39hb18efdd_1004   conda-forge/osx-arm64     Cached
  + bzip2                         1.0.8  h3422bc3_4          conda-forge/osx-arm64     Cached
  + ca-certificates         2022.5.18.1  h4653dfc_0          conda-forge/osx-arm64     Cached
  + certifi                 2022.5.18.1  py39h2804cbe_0      conda-forge/osx-arm64     Cached
  + cffi                         1.15.0  py39h52b1de0_0      conda-forge/osx-arm64     Cached
  + charset-normalizer           2.0.12  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + colorama                      0.4.4  pyh9f0ad1d_0        conda-forge/noarch        Cached
  + conda                        4.12.0  py39h2804cbe_0      conda-forge/osx-arm64     Cached
  + conda-package-handling        1.8.1  py39hb18efdd_1      conda-forge/osx-arm64     Cached
  + cryptography                 37.0.2  py39h4cb6239_0      conda-forge/osx-arm64     Cached
  + idna                            3.3  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + libffi                        3.4.2  h3422bc3_5          conda-forge/osx-arm64     Cached
  + libzlib                      1.2.12  h90dfc92_0          conda-forge/osx-arm64     Cached
  + ncurses                         6.3  h07bb92c_1          conda-forge/osx-arm64     Cached
  + openssl                      1.1.1o  ha287fd2_0          conda-forge/osx-arm64     Cached
  + pip                          22.1.2  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + pycosat                       0.6.3  py39hb18efdd_1010   conda-forge/osx-arm64     Cached
  + pycparser                      2.21  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + pyopenssl                    22.0.0  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + pysocks                       1.7.1  py39h2804cbe_5      conda-forge/osx-arm64     Cached
  + python                       3.9.13  hc596b02_0_cpython  conda-forge/osx-arm64     Cached
  + python_abi                      3.9  2_cp39              conda-forge/osx-arm64     Cached
  + readline                        8.1  hedafd6a_0          conda-forge/osx-arm64     Cached
  + requests                     2.27.1  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + ruamel_yaml                 0.15.80  py39h9eb174b_1007   conda-forge/osx-arm64     Cached
  + setuptools                   62.3.2  py39h2804cbe_0      conda-forge/osx-arm64     Cached
  + six                          1.16.0  pyh6c4a22f_0        conda-forge/noarch        Cached
  + sqlite                       3.38.5  h40dfcc0_0          conda-forge/osx-arm64     Cached
  + tk                           8.6.12  he1e0b03_0          conda-forge/osx-arm64     Cached
  + tqdm                         4.64.0  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + tzdata                        2022a  h191b570_0          conda-forge/noarch        Cached
  + urllib3                      1.26.9  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + wheel                        0.37.1  pyhd8ed1ab_0        conda-forge/noarch        Cached
  + xz                            5.2.5  h642e427_1          conda-forge/osx-arm64     Cached
  + yaml                          0.2.5  h3422bc3_2          conda-forge/osx-arm64     Cached
  + zlib                         1.2.12  h90dfc92_0          conda-forge/osx-arm64     Cached

  Summary:

  Install: 36 packages

  Total download: 0 B

───────────────────────────────────────────────────────────────────────────────────────────────


Transaction starting
Linking bzip2-1.0.8-h3422bc3_4
Linking ca-certificates-2022.5.18.1-h4653dfc_0
Linking libffi-3.4.2-h3422bc3_5
Linking libzlib-1.2.12-h90dfc92_0
Linking ncurses-6.3-h07bb92c_1
Linking xz-5.2.5-h642e427_1
Linking yaml-0.2.5-h3422bc3_2
Linking openssl-1.1.1o-ha287fd2_0
Linking zlib-1.2.12-h90dfc92_0
Linking tk-8.6.12-he1e0b03_0
Linking readline-8.1-hedafd6a_0
Linking sqlite-3.38.5-h40dfcc0_0
Linking tzdata-2022a-h191b570_0
Linking python-3.9.13-hc596b02_0_cpython
Linking python_abi-3.9-2_cp39
Linking setuptools-62.3.2-py39h2804cbe_0
Linking wheel-0.37.1-pyhd8ed1ab_0
Linking pip-22.1.2-pyhd8ed1ab_0
Linking six-1.16.0-pyh6c4a22f_0
Linking pycparser-2.21-pyhd8ed1ab_0
Linking idna-3.3-pyhd8ed1ab_0
Linking colorama-0.4.4-pyh9f0ad1d_0
Linking charset-normalizer-2.0.12-pyhd8ed1ab_0
Linking tqdm-4.64.0-pyhd8ed1ab_0
Linking ruamel_yaml-0.15.80-py39h9eb174b_1007
Linking pysocks-1.7.1-py39h2804cbe_5
Linking pycosat-0.6.3-py39hb18efdd_1010
Linking certifi-2022.5.18.1-py39h2804cbe_0
Linking cffi-1.15.0-py39h52b1de0_0
Linking conda-package-handling-1.8.1-py39hb18efdd_1
Linking cryptography-37.0.2-py39h4cb6239_0
Linking brotlipy-0.7.0-py39hb18efdd_1004
Linking pyopenssl-22.0.0-pyhd8ed1ab_0
Linking urllib3-1.26.9-pyhd8ed1ab_0
Linking requests-2.27.1-pyhd8ed1ab_0
Linking conda-4.12.0-py39h2804cbe_0
Transaction finished
installation finished.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... 
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - conda-forge/noarch::requests==2.27.1=pyhd8ed1ab_0
  - conda-forge/osx-arm64::brotlipy==0.7.0=py39hb18efdd_1004
  - conda-forge/osx-arm64::setuptools==62.3.2=py39h2804cbe_0
  - conda-forge/noarch::six==1.16.0=pyh6c4a22f_0
  - conda-forge/noarch::charset-normalizer==2.0.12=pyhd8ed1ab_0
  - conda-forge/osx-arm64::python==3.9.13=hc596b02_0_cpython
  - conda-forge/osx-arm64::sqlite==3.38.5=h40dfcc0_0
  - conda-forge/noarch::urllib3==1.26.9=pyhd8ed1ab_0
  - conda-forge/noarch::wheel==0.37.1=pyhd8ed1ab_0
  - conda-forge/osx-arm64::readline==8.1=hedafd6a_0
  - conda-forge/osx-arm64::ruamel_yaml==0.15.80=py39h9eb174b_1007
  - conda-forge/noarch::colorama==0.4.4=pyh9f0ad1d_0
  - conda-forge/osx-arm64::cffi==1.15.0=py39h52b1de0_0
  - conda-forge/noarch::pyopenssl==22.0.0=pyhd8ed1ab_0
  - conda-forge/noarch::tqdm==4.64.0=pyhd8ed1ab_0
  - conda-forge/noarch::pip==22.1.2=pyhd8ed1ab_0
  - conda-forge/noarch::idna==3.3=pyhd8ed1ab_0
  - conda-forge/osx-arm64::pysocks==1.7.1=py39h2804cbe_5
  - conda-forge/osx-arm64::pycosat==0.6.3=py39hb18efdd_1010
  - conda-forge/osx-arm64::cryptography==37.0.2=py39h4cb6239_0
  - conda-forge/osx-arm64::conda==4.12.0=py39h2804cbe_0
  - conda-forge/osx-arm64::python_abi==3.9=2_cp39
  - conda-forge/osx-arm64::conda-package-handling==1.8.1=py39hb18efdd_1
  - conda-forge/osx-arm64::certifi==2022.5.18.1=py39h2804cbe_0
  - conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0
done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 4.13.0

Please update conda by running

    $ conda update -n base conda



## Package Plan ##

  environment location: /private/tmp/RtmpQb4nKx/rr/Test

  added / updated specs:
    - conda


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.6.15  |       h4653dfc_0         149 KB  conda-forge
    libzlib-1.2.12             |       ha287fd2_1          48 KB  conda-forge
    openssl-1.1.1q             |       ha287fd2_0         1.8 MB  conda-forge
    zlib-1.2.12                |       ha287fd2_1          77 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         2.0 MB

The following packages will be UPDATED:

  ca-certificates                    2022.5.18.1-h4653dfc_0 --> 2022.6.15-h4653dfc_0
  libzlib                                 1.2.12-h90dfc92_0 --> 1.2.12-ha287fd2_1
  openssl                                 1.1.1o-ha287fd2_0 --> 1.1.1q-ha287fd2_0
  zlib                                    1.2.12-h90dfc92_0 --> 1.2.12-ha287fd2_1



Downloading and Extracting Packages

openssl-1.1.1q       | 1.8 MB    |            |   0% 
openssl-1.1.1q       | 1.8 MB    |            |   1% 
openssl-1.1.1q       | 1.8 MB    | ########## | 100% 
openssl-1.1.1q       | 1.8 MB    | ########## | 100% 

zlib-1.2.12          | 77 KB     |            |   0% 
zlib-1.2.12          | 77 KB     | ########## | 100% 

libzlib-1.2.12       | 48 KB     |            |   0% 
libzlib-1.2.12       | 48 KB     | ########## | 100% 

ca-certificates-2022 | 149 KB    |            |   0% 
ca-certificates-2022 | 149 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ '/private/tmp/RtmpQb4nKx/rr/Test/bin/conda' 'create' '--yes' '--name' 'r-reticulate' 'python=3.8' 'numpy' '--quiet' '-c' 'conda-forge'
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /private/tmp/RtmpQb4nKx/rr/Test/envs/r-reticulate

  added / updated specs:
    - numpy
    - python=3.8


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libblas-3.9.0              |15_osxarm64_openblas          13 KB  conda-forge
    libcblas-3.9.0             |15_osxarm64_openblas          12 KB  conda-forge
    libcxx-14.0.6              |       h04bba0f_0         1.3 MB  conda-forge
    libgfortran-5.0.0.dev0     |11_0_1_hf114ba7_23          19 KB  conda-forge
    libgfortran5-11.0.1.dev0   |      hf114ba7_23         901 KB  conda-forge
    liblapack-3.9.0            |15_osxarm64_openblas          12 KB  conda-forge
    libopenblas-0.3.20         |openmp_h2209c59_0         3.8 MB  conda-forge
    llvm-openmp-14.0.4         |       hd125106_0         297 KB  conda-forge
    numpy-1.23.0               |   py38he1fcd3f_0         5.9 MB  conda-forge
    openssl-3.0.5              |       ha287fd2_0         2.3 MB  conda-forge
    python-3.8.13              |hd3575e6_0_cpython        12.3 MB  conda-forge
    python_abi-3.8             |           2_cp38           4 KB  conda-forge
    readline-8.1.2             |       h46ed386_0         263 KB  conda-forge
    setuptools-63.1.0          |   py38h10201cd_0         1.3 MB  conda-forge
    sqlite-3.39.0              |       h40dfcc0_0         1.6 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        30.0 MB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h3422bc3_4
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2022.6.15-h4653dfc_0
  libblas            conda-forge/osx-arm64::libblas-3.9.0-15_osxarm64_openblas
  libcblas           conda-forge/osx-arm64::libcblas-3.9.0-15_osxarm64_openblas
  libcxx             conda-forge/osx-arm64::libcxx-14.0.6-h04bba0f_0
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
  libgfortran        conda-forge/osx-arm64::libgfortran-5.0.0.dev0-11_0_1_hf114ba7_23
  libgfortran5       conda-forge/osx-arm64::libgfortran5-11.0.1.dev0-hf114ba7_23
  liblapack          conda-forge/osx-arm64::liblapack-3.9.0-15_osxarm64_openblas
  libopenblas        conda-forge/osx-arm64::libopenblas-0.3.20-openmp_h2209c59_0
  libzlib            conda-forge/osx-arm64::libzlib-1.2.12-ha287fd2_1
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-14.0.4-hd125106_0
  ncurses            conda-forge/osx-arm64::ncurses-6.3-h07bb92c_1
  numpy              conda-forge/osx-arm64::numpy-1.23.0-py38he1fcd3f_0
  openssl            conda-forge/osx-arm64::openssl-3.0.5-ha287fd2_0
  pip                conda-forge/noarch::pip-22.1.2-pyhd8ed1ab_0
  python             conda-forge/osx-arm64::python-3.8.13-hd3575e6_0_cpython
  python_abi         conda-forge/osx-arm64::python_abi-3.8-2_cp38
  readline           conda-forge/osx-arm64::readline-8.1.2-h46ed386_0
  setuptools         conda-forge/osx-arm64::setuptools-63.1.0-py38h10201cd_0
  sqlite             conda-forge/osx-arm64::sqlite-3.39.0-h40dfcc0_0
  tk                 conda-forge/osx-arm64::tk-8.6.12-he1e0b03_0
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  xz                 conda-forge/osx-arm64::xz-5.2.5-h642e427_1
  zlib               conda-forge/osx-arm64::zlib-1.2.12-ha287fd2_1


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
* Miniconda has been successfully installed at "/tmp/RtmpQb4nKx/rr/Test".
The package "samtools" has no matches.
There are these packages and versions available: 

NULL

Quitting from lines 93-96 (Herper.Rmd) 
Error: processing vignette 'Herper.Rmd' failed with diagnostics:
The package and/or version are not available in conda. Check above for details.
--- failed re-building ‘Herper.Rmd’

--- re-building ‘QuickStart.Rmd’ using rmarkdown
--- finished re-building ‘QuickStart.Rmd’

SUMMARY: processing the following file failed:
  ‘Herper.Rmd’

Error: Vignette re-building failed.
Execution halted