Shuai Guo
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/DeMixT |
| git_branch: RELEASE_3_18 |
| git_last_commit: 27c62df |
| git_last_commit_date: 2023-10-24 11:12:18 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:09 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 536/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DeMixT 1.18.0 (landing page) Shuai Guo
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the DeMixT package: - 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: DeMixT |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeMixT_1.18.0.tar.gz |
| StartedAt: 2024-04-17 11:36:34 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 11:44:03 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 449.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DeMixT.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeMixT_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/DeMixT.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeMixT/DESCRIPTION’ ... OK
* this is package ‘DeMixT’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth',
'matrixcalc', 'rmarkdown', 'DSS', 'dendextend', 'psych', 'sva'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘DeMixT’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/DeMixT.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 startup messages can be suppressed ... 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
DeMixT_GS: no visible global function definition for ‘qchisq’
DeMixT_preprocessing: no visible global function definition for
‘quantile_normalization’
detect_suspicious_sample_by_hierarchical_clustering_2comp :
<anonymous>: no visible global function definition for ‘wilcox.test’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
global function definition for ‘prcomp’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
global function definition for ‘dist’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
global function definition for ‘hclust’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
global function definition for ‘par’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
global function definition for ‘as.dendrogram’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
global function definition for ‘legend’
plot_dim: no visible global function definition for ‘prcomp’
plot_dim: no visible global function definition for ‘rainbow’
plot_dim: no visible global function definition for ‘abline’
plot_dim: no visible global function definition for ‘segments’
plot_dim: no visible global function definition for ‘points’
plot_dim: no visible global function definition for ‘legend’
plot_sd: no visible global function definition for ‘par’
scale_normalization_75th_percentile: no visible global function
definition for ‘median’
simulate_2comp: no visible global function definition for ‘SimpleList’
simulate_2comp: no visible global function definition for ‘DataFrame’
simulate_3comp: no visible global function definition for ‘SimpleList’
simulate_3comp: no visible global function definition for ‘DataFrame’
Undefined global functions or variables:
DataFrame SimpleList abline as.dendrogram dist hclust legend median
par points prcomp qchisq quantile_normalization rainbow segments
wilcox.test
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "legend", "par", "points", "segments")
importFrom("stats", "as.dendrogram", "dist", "hclust", "median",
"prcomp", "qchisq", "wilcox.test")
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 ... WARNING
Undocumented arguments in documentation object 'detect_suspicious_sample_by_hierarchical_clustering_2comp'
‘labels’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DeMixT_S2 63.561 0.108 63.921
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘calibrate’
* 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: 2 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/DeMixT.Rcheck/00check.log’
for details.
DeMixT.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeMixT
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DeMixT.c -o DeMixT.o
DeMixT.c:37:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^
DeMixT.c:37:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^
DeMixT.c:37:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^
DeMixT.c:37:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
^
DeMixT.c:591:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^
DeMixT.c:591:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^
DeMixT.c:1280:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^
DeMixT.c:1280:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^
DeMixT.c:1307:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^
DeMixT.c:1307:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^
DeMixT.c:1322:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^
DeMixT.c:1322:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
double obj_old, obj_new;
^
12 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Profile_2D.cpp -o Profile_2D.o
Profile_2D.cpp:987:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i=1;
^
Profile_2D.cpp:1022:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i=1;
^
Profile_2D.cpp:1057:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i=1;
^
Profile_2D.cpp:1437:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i=1;
^
Profile_2D.cpp:1460:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i=1;
^
Profile_2D.cpp:1484:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i=1;
^
Profile_2D.cpp:1508:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i=1;
^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DeMixT.so DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-DeMixT/00new/DeMixT/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
** testing if installed package keeps a record of temporary installation path
* DONE (DeMixT)
DeMixT.Rcheck/DeMixT-Ex.timings
| name | user | system | elapsed | |
| DeMixT | 0.005 | 0.009 | 0.013 | |
| DeMixT_DE | 0.002 | 0.004 | 0.005 | |
| DeMixT_GS | 0.001 | 0.004 | 0.006 | |
| DeMixT_S2 | 63.561 | 0.108 | 63.921 | |
| Optimum_KernelC | 0.002 | 0.005 | 0.006 | |
| simulate_2comp | 1.293 | 0.027 | 1.324 | |
| simulate_3comp | 0.100 | 0.026 | 0.126 | |