===============================
BiocCheckGitClone('HiCool')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: HiCool
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCool/DESCRIPTION’ ... OK
* this is package ‘HiCool’ version ‘0.99.1’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiCool’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... 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 ... [23s/23s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [229s/216s] ERROR
Running examples in ‘HiCool-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HiCool
> ### Title: Processing Hi-C paired-end fastq files in R
> ### Aliases: HiCool importHiCoolFolder getHiCoolArgs getHicStats
>
> ### ** Examples
>
> r1 <- HiContactsData::HiContactsData(sample = 'yeast_wt', format = 'fastq_R1')
snapshotDate(): 2023-01-30
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
> r2 <- HiContactsData::HiContactsData(sample = 'yeast_wt', format = 'fastq_R2')
snapshotDate(): 2023-01-30
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
> hcf <- HiCool(r1, r2, genome = 'R64-1-1', output = './HiCool/')
HiCool :: Recovering bowtie2 genome index from AWS iGenomes...
HiCool :: Initiating processing of fastq files [tmp folder: /tmp/Rtmp8ONpPw/DA7WNR]...
HiCool :: Mapping fastq files...
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
[E::hts_open_format] Failed to open file "/tmp/Rtmp8ONpPw/DA7WNR/tmp/921822f8/temp_alignment.bam" : No such file or directory
Error: FileNotFoundError: [Errno 2] could not open alignment file `/tmp/Rtmp8ONpPw/DA7WNR/tmp/921822f8/temp_alignment.bam`: No such file or directory
Execution halted
Could not open index file /tmp/Rtmp8ONpPw/R64-1-1.1.bt2
Could not open index file /tmp/Rtmp8ONpPw/R64-1-1.2.bt2
Segmentation fault (core dumped)
(ERR): bowtie2-align exited with value 139
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [42s/24s]
[42s/24s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HiCool.R:9'): Check that HiCool works with AWS S3 iGenomes ─────
<Rcpp::exception/C++Error/error/condition>
Error: FileNotFoundError: [Errno 2] could not open alignment file `/tmp/RtmpvvUdJX/YAYMKA/tmp/d8c0f992/temp_alignment.bam`: No such file or directory
Backtrace:
▆
1. └─HiCool::HiCool(r1, r2, "R64-1-1", output = "./HiCool/") at test-HiCool.R:9:4
2. └─basilisk::basiliskRun(...)
3. └─HiCool (local) fun(...)
4. ├─base::write(...)
5. │ └─base::cat(...)
6. ├─reticulate::py_capture_output(...)
7. │ └─base::force(expr)
8. └─hs$pipeline$full_pipeline(...)
9. └─reticulate:::py_call_impl(callable, dots$args, dots$keywords)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
Error: Test failures
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 ... [2s/2s] OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiCool_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: HiCool
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/Rtmpn5ps5T/file3a324d2366cd7e/HiCool
─ installDir: /tmp/Rtmpn5ps5T/file3a324d6bbad83
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Normalization
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiCool...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 74 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 25 lines
(2%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES
See the HiCool.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
BiocCheckGitClone('HiCool')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: HiCool
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCool/DESCRIPTION’ ... OK
* this is package ‘HiCool’ version ‘0.99.1’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiCool’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... 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 ... [25s/25s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [215s/229s] ERROR
Running examples in ‘HiCool-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HiCReport
> ### Title: HiC processing report
> ### Aliases: HiCReport
>
> ### ** Examples
>
> mcool_path <- HiContactsData::HiContactsData('yeast_wt', 'mcool')
snapshotDate(): 2023-01-30
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
> pairs_path <- HiContactsData::HiContactsData('yeast_wt', 'pairs.gz')
snapshotDate(): 2023-01-30
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
> log_path <- HiContactsData::HiContactsData(sample = 'yeast_wt', format = 'HiCool_log')
snapshotDate(): 2023-01-30
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
> cf <- CoolFile(mcool_path, pairs = pairs_path, metadata = list(log = log_path))
> HiCReport(cf)
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: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env
added / updated specs:
- python=3.9.1
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/osx-64::ca-certificates-2022.12.7-h033912b_0
libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2
libsqlite conda-forge/osx-64::libsqlite-3.40.0-ha978bb4_0
libzlib conda-forge/osx-64::libzlib-1.2.13-hfd90126_4
ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
openssl conda-forge/osx-64::openssl-1.1.1s-hfd90126_1
pip conda-forge/noarch::pip-22.3.1-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.9.1-h2502468_5_cpython
readline conda-forge/osx-64::readline-8.1.2-h3899abd_0
setuptools conda-forge/noarch::setuptools-66.1.1-pyhd8ed1ab_0
sqlite conda-forge/osx-64::sqlite-3.40.0-h9ae0607_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
tzdata conda-forge/noarch::tzdata-2022g-h191b570_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-hfd90126_4
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: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env
added / updated specs:
- python=3.9.1
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hecd8cb5_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-1.1.1s-hfd90126_1 --> pkgs/main::openssl-1.1.1s-hca72f7f_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: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env
added / updated specs:
- bowtie2=2.4.5
- numpy=1.23.4
- python[version='3.9.1.*,3.9.1.*']
- samtools=1.7
The following NEW packages will be INSTALLED:
bowtie2 bioconda/osx-64::bowtie2-2.4.5-py39he245752_2
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
curl conda-forge/osx-64::curl-7.71.1-hbdca1c0_1
krb5 conda-forge/osx-64::krb5-1.17.2-h60d9502_0
libblas conda-forge/osx-64::libblas-3.9.0-16_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-16_osx64_openblas
libcurl conda-forge/osx-64::libcurl-7.71.1-he6690cf_1
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
libgfortran conda-forge/osx-64::libgfortran-5.0.0-11_3_0_h97931a8_27
libgfortran5 conda-forge/osx-64::libgfortran5-11.3.0-h082f757_27
liblapack conda-forge/osx-64::liblapack-3.9.0-16_osx64_openblas
libopenblas conda-forge/osx-64::libopenblas-0.3.21-openmp_h429af6e_3
libssh2 conda-forge/osx-64::libssh2-1.10.0-h52ee1ee_2
llvm-openmp conda-forge/osx-64::llvm-openmp-15.0.7-h61d9ccf_0
lz4-c conda-forge/osx-64::lz4-c-1.9.4-hf0c8a7f_0
numpy conda-forge/osx-64::numpy-1.23.4-py39hdfa1d0c_1
perl conda-forge/osx-64::perl-5.32.1-2_h0d85af4_perl5
python_abi conda-forge/osx-64::python_abi-3.9-3_cp39
samtools bioconda/osx-64::samtools-1.7-1
tbb conda-forge/osx-64::tbb-2020.2-h940c156_4
zstd conda-forge/osx-64::zstd-1.5.2-ha9df2e0_1
The following packages will be REMOVED:
libsqlite-3.40.0-ha978bb4_0
The following packages will be UPDATED:
openssl pkgs/main::openssl-1.1.1s-hca72f7f_0 --> conda-forge::openssl-1.1.1s-hfd90126_1
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-h033912b_0
The following packages will be DOWNGRADED:
libzlib 1.2.13-hfd90126_4 --> 1.2.11-h6c3fc93_1014
sqlite 3.40.0-h9ae0607_0 --> 3.38.5-hd9f0692_0
zlib 1.2.13-hfd90126_4 --> 1.2.11-h6c3fc93_1014
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: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting hicstuff==3.1.5
Using cached hicstuff-3.1.5-py3-none-any.whl (114 kB)
Collecting cooler==0.8.11
Using cached cooler-0.8.11-py2.py3-none-any.whl (100 kB)
Collecting chromosight==1.6.3
Using cached chromosight-1.6.3-py3-none-any.whl (144 kB)
Collecting pyfastx
Using cached pyfastx-0.9.1-cp39-cp39-macosx_10_9_x86_64.whl (789 kB)
Collecting scipy
Using cached scipy-1.10.0.tar.gz (42.4 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [73 lines of output]
The Meson build system
Version: 1.0.0
Source dir: /private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247
Build dir: /private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247/.mesonpy-l7pp8ozh/build
Build type: native build
Project name: SciPy
Project version: 1.10.0
C compiler for the host machine: cc (clang 11.0.0 "Apple clang version 11.0.0 (clang-1100.0.33.17)")
C linker for the host machine: cc ld64 530
C++ compiler for the host machine: c++ (clang 11.0.0 "Apple clang version 11.0.0 (clang-1100.0.33.17)")
C++ linker for the host machine: c++ ld64 530
Host machine cpu family: x86_64
Host machine cpu: x86_64
Compiler for C supports arguments -Wno-unused-but-set-variable: NO
Compiler for C supports arguments -Wno-unused-function: YES
Compiler for C supports arguments -Wno-conversion: YES
Compiler for C supports arguments -Wno-misleading-indentation: NO
Compiler for C supports arguments -Wno-incompatible-pointer-types: YES
Library m found: YES
Fortran compiler for the host machine: gfortran (gcc 8.2.0 "GNU Fortran (GCC) 8.2.0")
Fortran linker for the host machine: gfortran ld64 530
Compiler for Fortran supports arguments -Wno-conversion: YES
Checking if "-Wl,--version-script" : links: NO
Program cython found: YES (/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/bin/cython)
Program python found: YES (/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env/bin/python)
Found pkg-config: /usr/local/bin/pkg-config (0.29.2)
Program pythran found: YES (/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/bin/pythran)
Run-time dependency threads found: YES
Library npymath found: YES
Library npyrandom found: YES
Found CMake: /Applications/CMake.app/Contents/bin/cmake (3.23.0)
Run-time dependency openblas found: NO (tried pkgconfig, framework and cmake)
Run-time dependency openblas found: NO (tried pkgconfig, framework and cmake)
../../scipy/meson.build:134:0: ERROR: Dependency "OpenBLAS" not found, tried pkgconfig, framework and cmake
A full log can be found at /private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247/.mesonpy-l7pp8ozh/build/meson-logs/meson-log.txt
+ meson setup --prefix=/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env /private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247 /private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247/.mesonpy-l7pp8ozh/build --native-file=/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247/.mesonpy-native-file.ini -Ddebug=false -Doptimization=2
Traceback (most recent call last):
File "/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 144, in prepare_metadata_for_build_wheel
hook = backend.prepare_metadata_for_build_wheel
AttributeError: module 'mesonpy' has no attribute 'prepare_metadata_for_build_wheel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
main()
File "/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 148, in prepare_metadata_for_build_wheel
whl_basename = backend.build_wheel(metadata_directory, config_settings)
File "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 1060, in build_wheel
with _project(config_settings) as project:
File "/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env/lib/python3.9/contextlib.py", line 117, in __enter__
return next(self.gen)
File "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 975, in _project
with Project.with_temp_working_dir(
File "/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env/lib/python3.9/contextlib.py", line 117, in __enter__
return next(self.gen)
File "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 750, in with_temp_working_dir
yield cls(source_dir, tmpdir, build_dir, meson_args)
File "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 632, in __init__
self._configure(reconfigure=bool(build_dir) and not native_file_mismatch)
File "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 680, in _configure
self._meson('setup', *setup_args)
File "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 657, in _meson
return self._proc('meson', *args)
File "/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-build-env-uh8vct2j/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 652, in _proc
subprocess.check_call(list(args), env=self._env)
File "/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['meson', 'setup', '--prefix=/Users/pkgbuild/Library/Caches/org.R-project.R/R/basilisk/1.11.2/HiCool/0.99.1/env', '/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247', '/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247/.mesonpy-l7pp8ozh/build', '--native-file=/private/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T/pip-install-wm1mtez5/scipy_4fe8987eee324f4599fce67cbc03c247/.mesonpy-native-file.ini', '-Ddebug=false', '-Doptimization=2']' returned non-zero exit status 1.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Quitting from lines 202-217 (d369332250d6_7752.Rmd)
Error in setupBasiliskEnv(envpath, packages = .getPackages(env), channels = .getChannels(env), :
failed to install additional packages via pip
Calls: HiCReport ... <Anonymous> -> obtainEnvironmentPath -> setupBasiliskEnv
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [123s/128s]
[123s/128s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
snapshotDate(): 2023-01-30
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 2 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HiCool.R:9'): Check that HiCool works with AWS S3 iGenomes ─────
Error in `setupBasiliskEnv(envpath, packages = .getPackages(env), channels = .getChannels(env),
pip = .getPipPackages(env), paths = file.path(getSystemDir(pkgname,
installed = TRUE), .getPipPaths(env)))`: failed to install additional packages via pip
Backtrace:
▆
1. └─HiCool::HiCool(r1, r2, "R64-1-1", output = "./HiCool/") at test-HiCool.R:9:4
2. └─basilisk::basiliskStart(env_HiCool)
3. └─basilisk::obtainEnvironmentPath(env)
4. └─basilisk::setupBasiliskEnv(...)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 2 ]
Error: Test failures
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 ... [4s/4s] OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiCool_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: HiCool
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp0d2gpX/file92e2179f49d2/HiCool
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp0d2gpX/file92e22c55851c
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2879/0f9f3eb53ad1705af7cca934d10bfa951308fd96/HiCool.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Normalization
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiCool...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 74 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 25 lines
(2%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES
See the HiCool.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.