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This page was generated on 2023-04-12 10:55:32 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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

INSTALL results for Travel on nebbiolo1


To the developers/maintainers of the Travel package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Travel.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 2110/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Travel 1.7.0  (landing page)
Jiefei Wang
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/Travel
git_branch: devel
git_last_commit: 8ef40d3
git_last_commit_date: 2022-11-01 11:23:56 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  ERROR    ERROR  skipped
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: Travel
Version: 1.7.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Travel
StartedAt: 2023-04-11 15:03:10 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 15:03:42 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 31.5 seconds
RetCode: 1
Status:   ERROR  

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Travel
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘Travel’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Cpp_interface.cpp -o Cpp_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c altfile_operations.cpp -o altfile_operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c altmmap_operations.cpp -o altmmap_operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c altrep_manager.cpp -o altrep_manager.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c class_Cache_block.cpp -o class_Cache_block.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c class_Filesystem_cache_copier.cpp -o class_Filesystem_cache_copier.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c class_Filesystem_file_data.cpp -o class_Filesystem_file_data.o
In file included from class_Filesystem_file_data.h:5,
                 from class_Filesystem_file_data.cpp:1:
class_Cache_block.h:10:5: error: ‘size_t’ does not name a type
   10 |     size_t size;
      |     ^~~~~~
class_Cache_block.h:1:1: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
  +++ |+#include <cstddef>
    1 | #ifndef HEADER_CACHE_BLOCK
class_Cache_block.h:11:5: error: ‘size_t’ does not name a type
   11 |     size_t *counter = nullptr;
      |     ^~~~~~
class_Cache_block.h:11:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:14:23: error: expected ‘)’ before ‘size’
   14 |     Cache_block(size_t size);
      |                ~      ^~~~~
      |                       )
class_Cache_block.h:21:5: error: ‘size_t’ does not name a type
   21 |     size_t use_count() const;
      |     ^~~~~~
class_Cache_block.h:21:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:23:5: error: ‘size_t’ does not name a type
   23 |     size_t get_size() const;
      |     ^~~~~~
class_Cache_block.h:23:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:27:5: error: ‘size_t’ does not name a type
   27 |     size_t get_serialize_size() const;
      |     ^~~~~~
class_Cache_block.h:27:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Filesystem_file_data.cpp: In member function ‘size_t Filesystem_file_data::get_serialize_size()’:
class_Filesystem_file_data.cpp:70:26: error: ‘const class Cache_block’ has no member named ‘get_serialize_size’
   70 |         size += i.second.get_serialize_size();
      |                          ^~~~~~~~~~~~~~~~~~
class_Filesystem_file_data.cpp: In member function ‘void Filesystem_file_data::serialize(void*)’:
class_Filesystem_file_data.cpp:92:39: error: ‘const class Cache_block’ has no member named ‘get_serialize_size’
   92 |         size_t buffer_size = i.second.get_serialize_size();
      |                                       ^~~~~~~~~~~~~~~~~~
class_Filesystem_file_data.cpp: In member function ‘void Filesystem_cache_index_iterator::compute_block_info()’:
class_Filesystem_file_data.cpp:177:39: error: ‘class Cache_block’ has no member named ‘get_size’
  177 |     block_length = block_iter->second.get_size() / type_size;
      |                                       ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: class_Filesystem_file_data.o] Error 1
ERROR: compilation failed for package ‘Travel’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/Travel’