Thomas Carroll
| Snapshot Date: 2022-09-25 13:55:17 -0400 (Sun, 25 Sep 2022) |
| git_url: https://git.bioconductor.org/packages/Herper |
| git_branch: RELEASE_3_15 |
| git_last_commit: f903ed1 |
| git_last_commit_date: 2022-04-26 12:09:44 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-09-26 13:21:43 -0400 (Mon, 26 Sep 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4375 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4128 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4193 |
| 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 | ||||
|
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. |
| Package 887/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Herper 1.6.0 (landing page) Thomas Carroll
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | TIMEOUT | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| Package: Herper |
| Version: 1.6.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Herper.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Herper_1.6.0.tar.gz |
| StartedAt: 2022-09-26 01:41:35 -0400 (Mon, 26 Sep 2022) |
| EndedAt: 2022-09-26 01:59:55 -0400 (Mon, 26 Sep 2022) |
| EllapsedTime: 1100.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Herper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Herper.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Herper_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/Herper.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Herper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Herper' version '1.6.0'
* 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 whether package 'Herper' 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ListCondaEnvironments 0.16 0.72 335.45
UseEnvironments 0.14 0.40 188.65
install_CondaSysReqs 0.06 0.47 30.06
ListCondaPackages 0.03 0.12 13.53
SaveEnvironments 0.02 0.03 14.66
install_CondaTools 0.02 0.00 13.92
search_conda 0.00 0.01 13.71
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* 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: OK
Herper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Herper ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'Herper' ... ** using staged installation ** R ** 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 (Herper)
Herper.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> library(testthat)
> library(Herper)
Loading required package: reticulate
>
> test_check("Herper")
trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe'
Content type 'application/octet-stream' length 74687656 bytes (71.2 MB)
==================================================
downloaded 71.2 MB
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpeKFC5i\Test
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.07.19 | haa95532_0 123 KB
certifi-2022.9.14 | py39haa95532_0 155 KB
cffi-1.15.1 | py39h2bbff1b_0 218 KB
colorama-0.4.5 | py39haa95532_0 28 KB
conda-4.14.0 | py39haa95532_0 937 KB
conda-package-handling-1.9.0| py39h8cc25b3_0 726 KB
cryptography-37.0.1 | py39h21b164f_0 977 KB
cytoolz-0.11.0 | py39h2bbff1b_0 294 KB
openssl-1.1.1q | h2bbff1b_0 4.8 MB
pip-22.1.2 | py39haa95532_0 2.5 MB
requests-2.28.1 | py39haa95532_0 99 KB
setuptools-63.4.1 | py39haa95532_0 1.0 MB
sqlite-3.39.2 | h2bbff1b_0 805 KB
toolz-0.11.2 | pyhd3eb1b0_0 49 KB
tqdm-4.64.0 | py39haa95532_0 155 KB
tzdata-2022c | h04d1e81_0 107 KB
urllib3-1.26.11 | py39haa95532_0 184 KB
------------------------------------------------------------
Total: 13.1 MB
The following NEW packages will be INSTALLED:
cytoolz pkgs/main/win-64::cytoolz-0.11.0-py39h2bbff1b_0
toolz pkgs/main/noarch::toolz-0.11.2-pyhd3eb1b0_0
The following packages will be REMOVED:
conda-content-trust-0.1.1-pyhd3eb1b0_0
six-1.16.0-pyhd3eb1b0_1
The following packages will be UPDATED:
ca-certificates 2022.3.29-haa95532_1 --> 2022.07.19-haa95532_0
certifi 2021.10.8-py39haa95532_2 --> 2022.9.14-py39haa95532_0
cffi 1.15.0-py39h2bbff1b_1 --> 1.15.1-py39h2bbff1b_0
colorama pkgs/main/noarch::colorama-0.4.4-pyhd~ --> pkgs/main/win-64::colorama-0.4.5-py39haa95532_0
conda 4.12.0-py39haa95532_0 --> 4.14.0-py39haa95532_0
conda-package-han~ 1.8.1-py39h8cc25b3_0 --> 1.9.0-py39h8cc25b3_0
cryptography 36.0.0-py39h21b164f_0 --> 37.0.1-py39h21b164f_0
openssl 1.1.1n-h2bbff1b_0 --> 1.1.1q-h2bbff1b_0
pip 21.2.4-py39haa95532_0 --> 22.1.2-py39haa95532_0
requests pkgs/main/noarch::requests-2.27.1-pyh~ --> pkgs/main/win-64::requests-2.28.1-py39haa95532_0
setuptools 61.2.0-py39haa95532_0 --> 63.4.1-py39haa95532_0
sqlite 3.38.2-h2bbff1b_0 --> 3.39.2-h2bbff1b_0
tqdm pkgs/main/noarch::tqdm-4.63.0-pyhd3eb~ --> pkgs/main/win-64::tqdm-4.64.0-py39haa95532_0
tzdata 2022a-hda174b7_0 --> 2022c-h04d1e81_0
urllib3 pkgs/main/noarch::urllib3-1.26.8-pyhd~ --> pkgs/main/win-64::urllib3-1.26.11-py39haa95532_0
Downloading and Extracting Packages
cffi-1.15.1 | 218 KB | | 0%
cffi-1.15.1 | 218 KB | ########## | 100%
cffi-1.15.1 | 218 KB | ########## | 100%
openssl-1.1.1q | 4.8 MB | | 0%
openssl-1.1.1q | 4.8 MB | ########## | 100%
openssl-1.1.1q | 4.8 MB | ########## | 100%
certifi-2022.9.14 | 155 KB | | 0%
certifi-2022.9.14 | 155 KB | ########## | 100%
certifi-2022.9.14 | 155 KB | ########## | 100%
conda-package-handli | 726 KB | | 0%
conda-package-handli | 726 KB | ########## | 100%
conda-package-handli | 726 KB | ########## | 100%
tzdata-2022c | 107 KB | | 0%
tzdata-2022c | 107 KB | ########## | 100%
tzdata-2022c | 107 KB | ########## | 100%
cytoolz-0.11.0 | 294 KB | | 0%
cytoolz-0.11.0 | 294 KB | ########## | 100%
cytoolz-0.11.0 | 294 KB | ########## | 100%
pip-22.1.2 | 2.5 MB | | 0%
pip-22.1.2 | 2.5 MB | ########## | 100%
pip-22.1.2 | 2.5 MB | ########## | 100%
conda-4.14.0 | 937 KB | | 0%
conda-4.14.0 | 937 KB | ########## | 100%
conda-4.14.0 | 937 KB | ########## | 100%
tqdm-4.64.0 | 155 KB | | 0%
tqdm-4.64.0 | 155 KB | ########## | 100%
tqdm-4.64.0 | 155 KB | ########## | 100%
requests-2.28.1 | 99 KB | | 0%
requests-2.28.1 | 99 KB | ########## | 100%
requests-2.28.1 | 99 KB | ########## | 100%
toolz-0.11.2 | 49 KB | | 0%
toolz-0.11.2 | 49 KB | ########## | 100%
toolz-0.11.2 | 49 KB | ########## | 100%
sqlite-3.39.2 | 805 KB | | 0%
sqlite-3.39.2 | 805 KB | ########## | 100%
sqlite-3.39.2 | 805 KB | ########## | 100%
urllib3-1.26.11 | 184 KB | | 0%
urllib3-1.26.11 | 184 KB | ########## | 100%
urllib3-1.26.11 | 184 KB | ########## | 100%
ca-certificates-2022 | 123 KB | | 0%
ca-certificates-2022 | 123 KB | ########## | 100%
ca-certificates-2022 | 123 KB | ########## | 100%
setuptools-63.4.1 | 1.0 MB | | 0%
setuptools-63.4.1 | 1.0 MB | ########## | 100%
setuptools-63.4.1 | 1.0 MB | ########## | 100%
cryptography-37.0.1 | 977 KB | | 0%
cryptography-37.0.1 | 977 KB | ########## | 100%
cryptography-37.0.1 | 977 KB | ########## | 100%
colorama-0.4.5 | 28 KB | | 0%
colorama-0.4.5 | 28 KB | ########## | 100%
colorama-0.4.5 | 28 KB | ########## | 100%
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: F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpeKFC5i\Test\envs\r-reticulate
added / updated specs:
- numpy
- python=3.8
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | h8ffe710_4 149 KB conda-forge
ca-certificates-2022.9.24 | h5b45459_0 189 KB conda-forge
intel-openmp-2022.1.0 | h57928b3_3787 3.7 MB conda-forge
libblas-3.9.0 | 16_win64_mkl 5.6 MB conda-forge
libcblas-3.9.0 | 16_win64_mkl 5.6 MB conda-forge
libffi-3.4.2 | h8ffe710_5 41 KB conda-forge
liblapack-3.9.0 | 16_win64_mkl 5.6 MB conda-forge
libsqlite-3.39.3 | hcfcfb64_0 642 KB conda-forge
libzlib-1.2.12 | hcfcfb64_3 71 KB conda-forge
mkl-2022.1.0 | h6a75c08_874 182.7 MB conda-forge
numpy-1.23.3 | py38h8503d5b_0 6.3 MB conda-forge
openssl-3.0.5 | hcfcfb64_2 7.8 MB conda-forge
pip-22.2.2 | pyhd8ed1ab_0 1.5 MB conda-forge
python-3.8.13 |hcf16a7b_0_cpython 16.9 MB conda-forge
python_abi-3.8 | 2_cp38 4 KB conda-forge
setuptools-65.3.0 | pyhd8ed1ab_1 782 KB conda-forge
sqlite-3.39.3 | hcfcfb64_0 656 KB conda-forge
tbb-2021.5.0 | h91493d7_5 172 KB conda-forge
tk-8.6.12 | h8ffe710_0 3.5 MB conda-forge
ucrt-10.0.20348.0 | h57928b3_0 1.2 MB conda-forge
vc-14.2 | hb210afc_7 14 KB conda-forge
vs2015_runtime-14.29.30139 | h890b9b1_7 1.3 MB conda-forge
wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge
xz-5.2.6 | h8d14728_0 213 KB conda-forge
------------------------------------------------------------
Total: 244.7 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/win-64::bzip2-1.0.8-h8ffe710_4
ca-certificates conda-forge/win-64::ca-certificates-2022.9.24-h5b45459_0
intel-openmp conda-forge/win-64::intel-openmp-2022.1.0-h57928b3_3787
libblas conda-forge/win-64::libblas-3.9.0-16_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-16_win64_mkl
libffi conda-forge/win-64::libffi-3.4.2-h8ffe710_5
liblapack conda-forge/win-64::liblapack-3.9.0-16_win64_mkl
libsqlite conda-forge/win-64::libsqlite-3.39.3-hcfcfb64_0
libzlib conda-forge/win-64::libzlib-1.2.12-hcfcfb64_3
mkl conda-forge/win-64::mkl-2022.1.0-h6a75c08_874
numpy conda-forge/win-64::numpy-1.23.3-py38h8503d5b_0
openssl conda-forge/win-64::openssl-3.0.5-hcfcfb64_2
pip conda-forge/noarch::pip-22.2.2-pyhd8ed1ab_0
python conda-forge/win-64::python-3.8.13-hcf16a7b_0_cpython
python_abi conda-forge/win-64::python_abi-3.8-2_cp38
setuptools conda-forge/noarch::setuptools-65.3.0-pyhd8ed1ab_1
sqlite conda-forge/win-64::sqlite-3.39.3-hcfcfb64_0
tbb conda-forge/win-64::tbb-2021.5.0-h91493d7_5
tk conda-forge/win-64::tk-8.6.12-h8ffe710_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_7
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30139-h890b9b1_7
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/win-64::xz-5.2.6-h8d14728_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Retrieving notices: ...working... done
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
2.81 3.51 369.29
Herper.Rcheck/Herper-Ex.timings
| name | user | system | elapsed | |
| ListCondaEnvironments | 0.16 | 0.72 | 335.45 | |
| ListCondaPackages | 0.03 | 0.12 | 13.53 | |
| SaveEnvironments | 0.02 | 0.03 | 14.66 | |
| UseEnvironments | 0.14 | 0.40 | 188.65 | |
| install_CondaSysReqs | 0.06 | 0.47 | 30.06 | |
| install_CondaTools | 0.02 | 0.00 | 13.92 | |
| search_conda | 0.00 | 0.01 | 13.71 | |