Back to Multiple platform build/check report for BioC 3.17:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-10-16 11:35:10 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 39/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alabaster.base 1.0.0  (landing page)
Aaron Lun
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/alabaster.base
git_branch: RELEASE_3_17
git_last_commit: 97c0956
git_last_commit_date: 2023-04-25 11:42:44 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

INSTALL results for alabaster.base on nebbiolo1


To the developers/maintainers of the alabaster.base package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.base.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.

raw results


Summary

Package: alabaster.base
Version: 1.0.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL alabaster.base
StartedAt: 2023-10-15 15:12:46 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 15:13:41 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 55.7 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL alabaster.base
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘alabaster.base’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c check_csv.cpp -o check_csv.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c check_list.cpp -o check_list.o
In file included from ../inst/include/uzuki2/uzuki2.hpp:14,
                 from check_list.cpp:3:
../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const string&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]’:
../inst/include/uzuki2/parse_hdf5.hpp:442:50:   required from ‘std::shared_ptr<uzuki2::Base> uzuki2::Hdf5Parser::parse(const H5::Group&, const string&, Externals) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals; std::string = std::__cxx11::basic_string<char>]’
../inst/include/uzuki2/parse_hdf5.hpp:521:32:   required from here
../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
  227 |         for (int i = 0; i < len; ++i) {
      |                         ~~^~~~~
../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long long unsigned int’ [-Wsign-compare]
  295 |                 if (x < 0 || x >= levlen) {
      |                              ~~^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c load_csv.cpp -o load_csv.o
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::add_missing() [with T = std::complex<double>; comservatory::Type tt = comservatory::COMPLEX; RVector = Rcpp::Vector<15>]’:
load_csv.cpp:36:10:   required from here
load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   37 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::add_missing() [with T = bool; comservatory::Type tt = comservatory::BOOLEAN; RVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’:
load_csv.cpp:36:10:   required from here
load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::push_back(T) [with T = bool; comservatory::Type tt = comservatory::BOOLEAN; RVector = Rcpp::Vector<10, Rcpp::PreserveStorage>]’:
load_csv.cpp:27:10:   required from here
load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   28 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::add_missing() [with T = double; comservatory::Type tt = comservatory::NUMBER; RVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’:
load_csv.cpp:36:10:   required from here
load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   37 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::push_back(T) [with T = double; comservatory::Type tt = comservatory::NUMBER; RVector = Rcpp::Vector<14, Rcpp::PreserveStorage>]’:
load_csv.cpp:27:10:   required from here
load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   28 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::add_missing() [with T = std::__cxx11::basic_string<char>; comservatory::Type tt = comservatory::STRING; RVector = Rcpp::Vector<16>]’:
load_csv.cpp:36:10:   required from here
load_csv.cpp:37:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   37 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
load_csv.cpp: In instantiation of ‘void RFilledField<T, tt, RVector>::push_back(T) [with T = std::__cxx11::basic_string<char>; comservatory::Type tt = comservatory::STRING; RVector = Rcpp::Vector<16>]’:
load_csv.cpp:27:10:   required from here
load_csv.cpp:28:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   28 |         if (position >= store.size()) {
      |             ~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c load_list.cpp -o load_list.o
In file included from ../inst/include/uzuki2/uzuki2.hpp:14,
                 from load_list.cpp:3:
../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const string&) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::ExternalTracker<uzuki2::DummyExternals>; std::string = std::__cxx11::basic_string<char>]’:
../inst/include/uzuki2/parse_hdf5.hpp:442:50:   required from ‘std::shared_ptr<uzuki2::Base> uzuki2::Hdf5Parser::parse(const H5::Group&, const string&, Externals) [with Provisioner = uzuki2::DummyProvisioner; Externals = uzuki2::DummyExternals; std::string = std::__cxx11::basic_string<char>]’
../inst/include/uzuki2/parse_hdf5.hpp:521:32:   required from here
../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
  227 |         for (int i = 0; i < len; ++i) {
      |                         ~~^~~~~
../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long long unsigned int’ [-Wsign-compare]
  295 |                 if (x < 0 || x >= levlen) {
      |                              ~~^~~~~~~~~
../inst/include/uzuki2/parse_hdf5.hpp: In instantiation of ‘std::shared_ptr<uzuki2::Base> uzuki2::hdf5::parse_inner(const H5::Group&, Externals&, const string&) [with Provisioner = RProvisioner; Externals = uzuki2::ExternalTracker<RExternals>; std::string = std::__cxx11::basic_string<char>]’:
../inst/include/uzuki2/parse_hdf5.hpp:442:50:   required from ‘std::shared_ptr<uzuki2::Base> uzuki2::Hdf5Parser::parse(const H5::Group&, const string&, Externals) [with Provisioner = RProvisioner; Externals = RExternals; std::string = std::__cxx11::basic_string<char>]’
../inst/include/uzuki2/parse_hdf5.hpp:486:34:   required from ‘std::shared_ptr<uzuki2::Base> uzuki2::Hdf5Parser::parse(const string&, const string&, Externals) [with Provisioner = RProvisioner; Externals = RExternals; std::string = std::__cxx11::basic_string<char>]’
load_list.cpp:288:56:   required from here
../inst/include/uzuki2/parse_hdf5.hpp:227:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
  227 |         for (int i = 0; i < len; ++i) {
      |                         ~~^~~~~
../inst/include/uzuki2/parse_hdf5.hpp:295:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long long unsigned int’ [-Wsign-compare]
  295 |                 if (x < 0 || x >= levlen) {
      |                              ~~^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c write_scalar.cpp -o write_scalar.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o load_csv.o load_list.o write_scalar.o /home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-alabaster.base/00new/alabaster.base/libs
** 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
** 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 (alabaster.base)