Pascal Schlosser
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/netboost |
| git_branch: devel |
| git_last_commit: 511a0a6 |
| git_last_commit_date: 2023-10-24 11:14:09 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:41:02 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1398/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| netboost 2.11.0 (landing page) Pascal Schlosser
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the netboost package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netboost.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: netboost |
| Version: 2.11.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:netboost.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings netboost_2.11.0.tar.gz |
| StartedAt: 2024-03-28 07:47:29 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 07:52:00 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 271.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: netboost.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:netboost.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings netboost_2.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/netboost.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netboost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netboost’ version ‘2.11.0’
* 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 ... 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 ‘netboost’ can be installed ... WARNING
Found the following significant warnings:
boosting.cpp:415:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
boosting.cpp:415:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
boosting.cpp:645:44: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/netboost.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
not specified by mailto: nor contained in < >
use the Contact field instead
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocStyle’
All declared Imports should be used.
* 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 ... NOTE
checkRd: (-1) cpp_filter_step.Rd:19: Lost braces
19 | Must be initialised before using @see{filter_base}
| ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
nb_clust 15.047 0.204 15.279
cut_trees 14.680 0.207 14.919
nb_summary 14.178 0.052 14.254
tree_search 13.916 0.044 13.989
nb_mcupgma 13.606 0.076 13.714
nb_dist 13.262 0.095 13.385
nb_filter 9.297 0.024 9.337
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 7 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/netboost.Rcheck/00check.log’
for details.
netboost.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL netboost
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘netboost’ ...
** using staged installation
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking for x86 cpuid output... unknown
checking for x86-AVX xgetbv output... unknown
checking whether C compiler accepts -Wno-deprecated... yes
checking for strip... strip
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/mcupgma/clustering_util/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I/usr/local/include `/home/biocbuild/R/R-4.4-devel-2024.03.20/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I/usr/local/include `/home/biocbuild/R/R-4.4-devel-2024.03.20/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c boosting.cpp -o boosting.o
boosting.cpp: In constructor ‘Boosting::Boosting(const NumericMatrix&, unsigned int, double)’:
boosting.cpp:415:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
415 | Rprintf( " DATA POINTER REAL LENGTH: %li / %li dbl (matrix: %d -- max %d)\n",
| ~^
| |
| int
| %ld
......
418 | (col+1) * nrow,
| ~~~~~~~~~~~~~~
| |
| size_t {aka long unsigned int}
boosting.cpp:415:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
415 | Rprintf( " DATA POINTER REAL LENGTH: %li / %li dbl (matrix: %d -- max %d)\n",
| ~^
| |
| int
| %ld
......
419 | (col+1) * (nrow + 256/sizeof(double))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| size_t {aka long unsigned int}
boosting.cpp: In instantiation of ‘Rcpp::IntegerVector Boosting::filter_column_gen(size_t) [with bool AVX = true; bool FMA = false; bool ALIGNED = true; Rcpp::IntegerVector = Rcpp::Vector<13>; size_t = long unsigned int]’:
boosting.cpp:729:61: required from here
boosting.cpp:645:44: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
645 | Rprintf( "C STEP: %d (ACTUAL_SEL: %d, UPDATE: %f)\n ",
| ~^
| |
| int
| %ld
646 | bstep + 1, actual_sel + 1, actual_update);
| ~~~~~~~~~~~~~~
| |
| size_t {aka long unsigned int}
boosting.cpp: In instantiation of ‘Rcpp::IntegerVector Boosting::filter_column_gen(size_t) [with bool AVX = false; bool FMA = false; bool ALIGNED = true; Rcpp::IntegerVector = Rcpp::Vector<13>; size_t = long unsigned int]’:
boosting.cpp:732:62: required from here
boosting.cpp:645:44: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
645 | Rprintf( "C STEP: %d (ACTUAL_SEL: %d, UPDATE: %f)\n ",
| ~^
| |
| int
| %ld
646 | bstep + 1, actual_sel + 1, actual_update);
| ~~~~~~~~~~~~~~
| |
| size_t {aka long unsigned int}
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I/usr/local/include `/home/biocbuild/R/R-4.4-devel-2024.03.20/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c dist_tom.cpp -o dist_tom.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I/usr/local/include `/home/biocbuild/R/R-4.4-devel-2024.03.20/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c tree_sort.cpp -o tree_sort.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -L/usr/local/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
strip -S netboost.so
installing via 'install.libs.R' to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC: /home/biocbuild/bbs-3.19-bioc/meat/netboost"
[1] "R_PACKAGE_DIR: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-netboost/00new/netboost"
[1] "R_ARCH: "
[1] "SHLIB_EXT: .so"
[1] "INSTALL PATH: /home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma/scripts/install_path.mk"
make: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma'
Clean build.
make: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma'
make: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma'
==== compiling clustering_util sources using external Makefile (clustering_util/Makefile) recursively
make -C clustering_util -f Makefile mcupgma_install
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma/clustering_util'
mkdir -p bin
mkdir -p obj.aarch64_Linux
g++ -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c
g++ -Wall -Wno-deprecated -O3 -DNDEBUG -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/ClusteringUtil.o ClusteringUtil.cpp
g++ -Wall -Wno-deprecated -O3 -DNDEBUG -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/Tree.o Tree.cpp
g++ -Wall -Wno-deprecated -O3 -DNDEBUG -o bin/edges2valid_clusters HashingMergerMain.cpp obj.aarch64_Linux/HashingMergerMain.cmdline.o obj.aarch64_Linux/ClusteringUtil.o obj.aarch64_Linux/Tree.o
g++ -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c
g++ -Wall -Wno-deprecated -O3 -DNDEBUG -o bin/edge_collator EdgeCollatorMain.cpp obj.aarch64_Linux/EdgeCollatorMain.cmdline.o obj.aarch64_Linux/ClusteringUtil.o obj.aarch64_Linux/Tree.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma/clustering_util'
==== compiling sources using external Makefile (clustering_round/Makefile) recursively
make -C clustering_round -f Makefile
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma/clustering_round'
mkdir -p dep.aarch64_Linux
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/test_heap.d obj.aarch64_Linux/test_heap.o obj.aarch64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.aarch64_Linux/test_heap.d
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o obj.aarch64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/HierarchicalClustering_main.d obj.aarch64_Linux/HierarchicalClustering_main.o obj.aarch64_Linux.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.aarch64_Linux/HierarchicalClustering_main.d
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/test_heap.d obj.aarch64_Linux/test_heap.o obj.aarch64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.aarch64_Linux/test_heap.d
test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o obj.aarch64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d
mkdir -p obj.aarch64_Linux
mkdir -p bin
g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.aarch64_Linux/HierarchicalClustering_main.o
cc -O3 -I./ -c HierarchicalClustering_main.cmdline.c -o obj.aarch64_Linux/HierarchicalClustering_main.cmdline.o
g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o
g++ obj.aarch64_Linux/HierarchicalClustering_main.o obj.aarch64_Linux/HierarchicalClustering_main.cmdline.o obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o -o bin/hierarchical_clustering -O3
g++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.aarch64_Linux/test_heap.o
cc -O3 -I./ -c test_heap.cmdline.c -o obj.aarch64_Linux/test_heap.cmdline.o
g++ obj.aarch64_Linux/test_heap.o obj.aarch64_Linux/test_heap.cmdline.o -o bin/test_heap -O3
make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma/clustering_round'
make: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma'
[1] "SRC: /home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma"
[1] "DEST: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.19-bioc/meat/netboost/src/mcupgma/scripts TO: /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "netboost.so"
** R
** data
*** moving datasets to lazyload DB
** 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 (netboost)
netboost.Rcheck/netboost-Ex.timings
| name | user | system | elapsed | |
| cut_trees | 14.680 | 0.207 | 14.919 | |
| dot-onAttach | 0 | 0 | 0 | |
| mcupgma_exec | 0.025 | 0.004 | 0.037 | |
| nb_clust | 15.047 | 0.204 | 15.279 | |
| nb_dist | 13.262 | 0.095 | 13.385 | |
| nb_filter | 9.297 | 0.024 | 9.337 | |
| nb_mcupgma | 13.606 | 0.076 | 13.714 | |
| nb_plot_dendro | 2.249 | 0.012 | 2.265 | |
| nb_summary | 14.178 | 0.052 | 14.254 | |
| nb_transfer | 2.281 | 0.000 | 2.284 | |
| netboost | 2.293 | 0.000 | 2.298 | |
| tree_search | 13.916 | 0.044 | 13.989 | |