##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dasper
###
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* checking for file ‘dasper/DESCRIPTION’ ... OK
* preparing ‘dasper’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dasper.Rmd’ using rmarkdown
unsorted interval: chr21 26021921 26022042
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 84
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 26021921 26022042
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 84
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 6456880 6456950
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 4
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 6456880 6456950
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 4
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
2 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 624
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
2 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 624
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 25880549 26171128
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 22
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 25880549 26171128
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 22
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 26021921 26022042
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 84
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 26021921 26022042
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 84
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 26021921 26022042
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 84
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 6456880 6456950
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 4
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 6456880 6456950
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 4
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 6456880 6456950
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 4
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
2 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 624
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
2 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 624
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
2 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 624
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 25880549 26171128
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 22
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 25880549 26171128
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 22
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
unsorted interval: chr21 25880549 26171128
, falling back to slower matching (doesn't affect BAM processing)
For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth.
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
total number of annotations in collapsed: 22
Processing /home/biocbuild/.cache/R/BiocFileCache/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/dasper/1.9.1/env_sklearn
added / updated specs:
- python=3.8.13
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
ca-certificates conda-forge/linux-64::ca-certificates-2022.12.7-ha878542_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19
libgomp conda-forge/linux-64::libgomp-12.2.0-h65d4601_19
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libsqlite conda-forge/linux-64::libsqlite-3.40.0-h753d276_0
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libzlib conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
openssl conda-forge/linux-64::openssl-3.1.0-h0b41bf4_0
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.8.13-ha86cf86_0_cpython
readline conda-forge/linux-64::readline-8.2-h8228510_1
setuptools conda-forge/noarch::setuptools-67.6.1-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.40.0-h4ff8645_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
wheel conda-forge/noarch::wheel-0.40.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/dasper/1.9.1/env_sklearn
added / updated specs:
- python=3.8.13
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-h06a4308_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.3.1
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/dasper/1.9.1/env_sklearn
added / updated specs:
- pandas=0.25.3
- python=3.8.13
- scikit-learn=0.23.2
The following NEW packages will be INSTALLED:
brotlipy conda-forge/linux-64::brotlipy-0.7.0-py38h0a891b7_1005
certifi conda-forge/noarch::certifi-2022.12.7-pyhd8ed1ab_0
cffi conda-forge/linux-64::cffi-1.15.1-py38h4a40e3a_3
charset-normalizer conda-forge/noarch::charset-normalizer-2.1.1-pyhd8ed1ab_0
cryptography conda-forge/linux-64::cryptography-40.0.1-py38h3d167d9_0
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
joblib conda-forge/noarch::joblib-1.2.0-pyhd8ed1ab_0
libblas conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-12.2.0-h69a702a_19
libgfortran5 conda-forge/linux-64::libgfortran5-12.2.0-h337968e_19
liblapack conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_3
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19
numpy conda-forge/linux-64::numpy-1.24.2-py38h10c12cc_0
packaging conda-forge/noarch::packaging-23.0-pyhd8ed1ab_0
pandas conda-forge/linux-64::pandas-0.25.3-py38hb3f55d8_0
platformdirs conda-forge/noarch::platformdirs-3.2.0-pyhd8ed1ab_0
pooch conda-forge/noarch::pooch-1.7.0-pyha770c72_3
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pyopenssl conda-forge/noarch::pyopenssl-23.1.1-pyhd8ed1ab_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.8-3_cp38
pytz conda-forge/noarch::pytz-2023.3-pyhd8ed1ab_0
requests conda-forge/noarch::requests-2.28.2-pyhd8ed1ab_0
scikit-learn conda-forge/linux-64::scikit-learn-0.23.2-py38h5d63f67_3
scipy conda-forge/linux-64::scipy-1.10.1-py38h10c12cc_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
threadpoolctl conda-forge/noarch::threadpoolctl-3.1.0-pyh8a188c0_0
typing-extensions conda-forge/noarch::typing-extensions-4.5.0-hd8ed1ab_0
typing_extensions conda-forge/noarch::typing_extensions-4.5.0-pyha770c72_0
urllib3 conda-forge/noarch::urllib3-1.26.15-pyhd8ed1ab_0
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2022.12.7-ha878542_0
setuptools conda-forge/noarch::setuptools-67.6.1~ --> conda-forge/linux-64::setuptools-59.8.0-py38h578d9bd_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 23.3.1
Please update conda by running
$ conda update -n base -c defaults conda
Quitting from lines 284-291 (dasper.Rmd)
Error: processing vignette 'dasper.Rmd' failed with diagnostics:
BiocParallel errors
1 remote errors, element index: 1
1 unevaluated and other errors
first remote error:
Error in eval(expr, envir, enclos): AttributeError: module 'sklearn' has no attribute 'ensemble'
--- failed re-building ‘dasper.Rmd’
SUMMARY: processing the following file failed:
‘dasper.Rmd’
Error: Vignette re-building failed.
Execution halted