Xiuyu Ma
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/EBSeq |
| git_branch: RELEASE_3_18 |
| git_last_commit: f1d4e44 |
| git_last_commit_date: 2023-10-24 09:54:07 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:41 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 | ||||
| Package 620/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EBSeq 2.0.0 (landing page) Xiuyu Ma
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the EBSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EBSeq.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: EBSeq |
| Version: 2.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBSeq_2.0.0.tar.gz |
| StartedAt: 2024-03-28 02:18:08 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 02:20:15 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 126.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: EBSeq.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBSeq_2.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/EBSeq.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBSeq’ version ‘2.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘EBSeq’ can be installed ... WARNING
Found the following significant warnings:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/EBSeq.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
DenNHist: no visible global function definition for ‘hist’
DenNHist: no visible global function definition for ‘lines’
DenNHist: no visible global function definition for ‘dbeta’
DenNHist: no visible global function definition for ‘legend’
EBMultiTest : <anonymous>: no visible global function definition for
‘quantile’
EBMultiTest: no visible binding for global variable ‘var’
EBMultiTest: no visible binding for global variable ‘NumBin’
EBMultiTest: no visible global function definition for ‘quantile’
EBMultiTest: no visible binding for global variable ‘PoolLower’
EBMultiTest: no visible binding for global variable ‘PoolUpper’
EBMultiTest : <anonymous>: no visible binding for global variable ‘var’
EBMultiTest: no visible binding for global variable ‘Print’
EBTest : <anonymous>: no visible global function definition for
‘quantile’
EBTest: no visible binding for global variable ‘var’
EBTest: no visible global function definition for ‘quantile’
EBTest: no visible binding for global variable ‘PoolLower’
EBTest: no visible binding for global variable ‘PoolUpper’
EBTest: no visible binding for global variable ‘Print’
GetDEResults: no visible binding for global variable ‘median’
LogN: no visible global function definition for ‘optim’
LogNMulti: no visible global function definition for ‘optim’
MedianNorm : <anonymous>: no visible global function definition for
‘median’
MedianNorm : <anonymous> : <anonymous>: no visible global function
definition for ‘median’
PlotPattern: no visible global function definition for ‘par’
PlotPattern: no visible global function definition for ‘rainbow’
PlotPattern: no visible global function definition for ‘heatmap’
PlotPostVsRawFC: no visible global function definition for ‘par’
PlotPostVsRawFC: no visible global function definition for ‘abline’
PlotPostVsRawFC: no visible global function definition for ‘rect’
PolyFitPlot: no visible global function definition for ‘lm’
PolyFitPlot: no visible global function definition for ‘smoothScatter’
PolyFitPlot: no visible global function definition for ‘axis’
PolyFitPlot: no visible global function definition for ‘lines’
QQP: no visible global function definition for ‘rbeta’
QQP: no visible global function definition for ‘qqplot’
QQP: no visible global function definition for ‘lm’
QQP: no visible global function definition for ‘abline’
QuantileNorm : <anonymous>: no visible global function definition for
‘quantile’
beta.mom: no visible global function definition for ‘var’
Undefined global functions or variables:
NumBin PoolLower PoolUpper Print abline axis dbeta heatmap hist
legend lines lm median optim par qqplot quantile rainbow rbeta rect
smoothScatter var
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
"par", "rect", "smoothScatter")
importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim",
"qqplot", "quantile", "rbeta", "var")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc/meat/EBSeq.Rcheck/00check.log’
for details.
EBSeq.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EBSeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘EBSeq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rexport.cpp -o Rexport.o
In file included from Rexport.cpp:11:
In file included from ./negativeBinomial.hpp:5:
In file included from ./agglomerativeClustering.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/tools/series.hpp:16:
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/tools/config.hpp:23:6: warning: "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-W#warnings]
# warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
^
In file included from Rexport.cpp:11:
./negativeBinomial.hpp:139:26: warning: variable 'maxholder' set but not used [-Wunused-but-set-variable]
auto maxholder = add.maxCoeff(&maxRow, &maxCol);
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o EBSeq.so Rexport.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-EBSeq/00new/EBSeq/libs
** R
** data
** demo
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EBSeq)
EBSeq.Rcheck/EBSeq-Ex.timings
| name | user | system | elapsed | |
| DenNHist | 1.528 | 0.032 | 1.798 | |
| EBMultiTest | 0.355 | 0.007 | 0.406 | |
| EBSeq_NingLeng-package | 0.182 | 0.006 | 0.209 | |
| EBTest | 0.619 | 0.008 | 0.684 | |
| GeneMat | 0.003 | 0.003 | 0.006 | |
| GetDEResults | 0.188 | 0.006 | 0.206 | |
| GetMultiFC | 0.104 | 0.006 | 0.112 | |
| GetMultiPP | 0.117 | 0.004 | 0.138 | |
| GetNg | 0.012 | 0.003 | 0.018 | |
| GetNormalizedMat | 0.010 | 0.004 | 0.014 | |
| GetPPMat | 0.182 | 0.007 | 0.202 | |
| GetPatterns | 0.001 | 0.001 | 0.002 | |
| GetSelectedPatterns | 0.344 | 0.006 | 0.388 | |
| IsoList | 0.005 | 0.003 | 0.009 | |
| IsoMultiList | 0.003 | 0.002 | 0.005 | |
| Likefun | 0.000 | 0.001 | 0.000 | |
| LikefunMulti | 0.000 | 0.001 | 0.000 | |
| LogN | 0.000 | 0.001 | 0.001 | |
| LogNMulti | 0.000 | 0.001 | 0.001 | |
| MedianNorm | 0.006 | 0.003 | 0.011 | |
| MultiGeneMat | 0.002 | 0.002 | 0.005 | |
| PlotPattern | 0.012 | 0.001 | 0.014 | |
| PlotPostVsRawFC | 0.215 | 0.007 | 0.242 | |
| PolyFitPlot | 0.018 | 0.006 | 0.026 | |
| PostFC | 0.180 | 0.007 | 0.213 | |
| QQP | 0.411 | 0.010 | 0.459 | |
| QuantileNorm | 0.009 | 0.003 | 0.012 | |
| RankNorm | 0.013 | 0.003 | 0.017 | |
| beta.mom | 0.000 | 0.000 | 0.001 | |
| crit_fun | 0.205 | 0.006 | 0.229 | |
| f0 | 0 | 0 | 0 | |
| f1 | 0 | 0 | 0 | |