Thomas Carroll
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/Herper |
| git_branch: master |
| git_last_commit: bedcb72 |
| git_last_commit_date: 2021-10-26 13:04:02 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:44 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 865/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Herper 1.5.0 (landing page) Thomas Carroll
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | TIMEOUT | skipped | |||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| 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: 1.5.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Herper.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Herper_1.5.0.tar.gz |
| StartedAt: 2022-03-17 19:18:17 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:30:55 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 758.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Herper.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Herper.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Herper_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Herper.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Herper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Herper' version '1.5.0'
* 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 0.11 0.47 209.76
UseEnvironments 0.06 0.28 125.34
install_CondaSysReqs 0.06 0.16 22.16
ListCondaPackages 0.05 0.01 8.49
SaveEnvironments 0.02 0.00 10.06
install_CondaTools 0.00 0.00 9.53
search_conda 0.00 0.00 7.78
* 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:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Herper
###
##############################################################################
##############################################################################
* installing to library 'D:/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
converting help for package 'Herper'
finding HTML links ... done
ListCondaEnvironments html
ListCondaPackages html
SaveEnvironments html
UseEnvironments html
conda_create_silentJSON html
conda_install_silentJSON html
install_CondaSysReqs html
install_CondaTools html
search_conda html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'Rhdf5lib' is missing or broken
done
Herper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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'
length 73787936 bytes (70.4 MB)
==================================================
downloaded 70.4 MB
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp2LmcVJ\Test
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.2.1 | haa95532_0 123 KB
cffi-1.15.0 | py39h2bbff1b_1 224 KB
colorama-0.4.4 | pyhd3eb1b0_0 21 KB
conda-4.12.0 | py39haa95532_0 14.5 MB
pyopenssl-22.0.0 | pyhd3eb1b0_0 50 KB
six-1.16.0 | pyhd3eb1b0_1 18 KB
sqlite-3.38.0 | h2bbff1b_0 807 KB
tqdm-4.63.0 | pyhd3eb1b0_0 84 KB
urllib3-1.26.8 | pyhd3eb1b0_0 106 KB
------------------------------------------------------------
Total: 15.9 MB
The following NEW packages will be INSTALLED:
colorama pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
The following packages will be REMOVED:
conda-content-trust-0.1.1-pyhd3eb1b0_0
The following packages will be UPDATED:
ca-certificates 2021.10.26-haa95532_2 --> 2022.2.1-haa95532_0
cffi 1.15.0-py39h2bbff1b_0 --> 1.15.0-py39h2bbff1b_1
conda 4.11.0-py39haa95532_0 --> 4.12.0-py39haa95532_0
pyopenssl 21.0.0-pyhd3eb1b0_1 --> 22.0.0-pyhd3eb1b0_0
six 1.16.0-pyhd3eb1b0_0 --> 1.16.0-pyhd3eb1b0_1
sqlite 3.37.0-h2bbff1b_0 --> 3.38.0-h2bbff1b_0
tqdm 4.62.3-pyhd3eb1b0_1 --> 4.63.0-pyhd3eb1b0_0
urllib3 1.26.7-pyhd3eb1b0_0 --> 1.26.8-pyhd3eb1b0_0
Downloading and Extracting Packages
ca-certificates-2022 | 123 KB | | 0%
ca-certificates-2022 | 123 KB | #3 | 13%
ca-certificates-2022 | 123 KB | ########## | 100%
urllib3-1.26.8 | 106 KB | | 0%
urllib3-1.26.8 | 106 KB | ########## | 100%
urllib3-1.26.8 | 106 KB | ########## | 100%
cffi-1.15.0 | 224 KB | | 0%
cffi-1.15.0 | 224 KB | ########## | 100%
cffi-1.15.0 | 224 KB | ########## | 100%
pyopenssl-22.0.0 | 50 KB | | 0%
pyopenssl-22.0.0 | 50 KB | ########## | 100%
pyopenssl-22.0.0 | 50 KB | ########## | 100%
conda-4.12.0 | 14.5 MB | | 0%
conda-4.12.0 | 14.5 MB | 4 | 4%
conda-4.12.0 | 14.5 MB | ##4 | 24%
conda-4.12.0 | 14.5 MB | ###6 | 37%
conda-4.12.0 | 14.5 MB | ####6 | 47%
conda-4.12.0 | 14.5 MB | ######2 | 62%
conda-4.12.0 | 14.5 MB | ########## | 100%
conda-4.12.0 | 14.5 MB | ########## | 100%
tqdm-4.63.0 | 84 KB | | 0%
tqdm-4.63.0 | 84 KB | ########## | 100%
tqdm-4.63.0 | 84 KB | ########## | 100%
sqlite-3.38.0 | 807 KB | | 0%
sqlite-3.38.0 | 807 KB | ########9 | 89%
sqlite-3.38.0 | 807 KB | ########## | 100%
six-1.16.0 | 18 KB | | 0%
six-1.16.0 | 18 KB | ########## | 100%
six-1.16.0 | 18 KB | ########## | 100%
colorama-0.4.4 | 21 KB | | 0%
colorama-0.4.4 | 21 KB | ########## | 100%
colorama-0.4.4 | 21 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: D:\biocbuild\bbs-3.15-bioc\tmpdir\Rtmp2LmcVJ\Test\envs\r-reticulate
added / updated specs:
- numpy
- python=3.8
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2021.10.8 | h5b45459_0 176 KB conda-forge
intel-openmp-2022.0.0 | h57928b3_3663 3.6 MB conda-forge
libblas-3.9.0 | 13_win64_mkl 5.3 MB conda-forge
libcblas-3.9.0 | 13_win64_mkl 5.3 MB conda-forge
liblapack-3.9.0 | 13_win64_mkl 5.3 MB conda-forge
mkl-2022.0.0 | h0e2418a_796 181.9 MB conda-forge
numpy-1.22.3 | py38hcf66579_0 6.1 MB conda-forge
openssl-3.0.0 | h8ffe710_2 10.0 MB conda-forge
pip-22.0.4 | pyhd8ed1ab_0 1.5 MB conda-forge
python-3.8.12 |h900ac77_2_cpython 19.3 MB conda-forge
python_abi-3.8 | 2_cp38 4 KB conda-forge
setuptools-60.10.0 | py38haa244fe_0 1.2 MB conda-forge
sqlite-3.37.1 | h8ffe710_0 1.2 MB conda-forge
tbb-2021.5.0 | h2d74725_0 148 KB conda-forge
ucrt-10.0.20348.0 | h57928b3_0 1.2 MB conda-forge
vc-14.2 | hb210afc_6 13 KB conda-forge
vs2015_runtime-14.29.30037 | h902a5da_6 1.3 MB conda-forge
wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge
------------------------------------------------------------
Total: 243.4 MB
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.10.8-h5b45459_0
intel-openmp conda-forge/win-64::intel-openmp-2022.0.0-h57928b3_3663
libblas conda-forge/win-64::libblas-3.9.0-13_win64_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-13_win64_mkl
liblapack conda-forge/win-64::liblapack-3.9.0-13_win64_mkl
mkl conda-forge/win-64::mkl-2022.0.0-h0e2418a_796
numpy conda-forge/win-64::numpy-1.22.3-py38hcf66579_0
openssl conda-forge/win-64::openssl-3.0.0-h8ffe710_2
pip conda-forge/noarch::pip-22.0.4-pyhd8ed1ab_0
python conda-forge/win-64::python-3.8.12-h900ac77_2_cpython
python_abi conda-forge/win-64::python_abi-3.8-2_cp38
setuptools conda-forge/win-64::setuptools-60.10.0-py38haa244fe_0
sqlite conda-forge/win-64::sqlite-3.37.1-h8ffe710_0
tbb conda-forge/win-64::tbb-2021.5.0-h2d74725_0
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_6
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_6
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
1.60 2.09 263.78
Herper.Rcheck/Herper-Ex.timings
| name | user | system | elapsed | |
| ListCondaEnvironments | 0.11 | 0.47 | 209.76 | |
| ListCondaPackages | 0.05 | 0.01 | 8.49 | |
| SaveEnvironments | 0.02 | 0.00 | 10.06 | |
| UseEnvironments | 0.06 | 0.28 | 125.34 | |
| install_CondaSysReqs | 0.06 | 0.16 | 22.16 | |
| install_CondaTools | 0.00 | 0.00 | 9.53 | |
| search_conda | 0.00 | 0.00 | 7.78 | |