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URL: https://git.bioconductor.org/packages/pgen2gds

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo1 Summary

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Package: pgen2gds

Version: 0.99.1

RVersion: 4.6

BiocVersion: 3.23

BuildCommand: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data pgen2gds

BuildTime: 0 minutes 1.47 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: pgen2gds_20260518181045

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: pgen2gds. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 1. Build Package status: 1.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file pgen2gds/DESCRIPTION ... OK
* preparing pgen2gds:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
      -----------------------------------
* installing *source* package pgen2gds ...
** this is package pgen2gds version 0.99.1
** using staged installation
** libs
using C compiler: gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
using C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_pgen2gds.c -o R_pgen2gds.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/gdsfmt/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pgen2gds.cpp -o pgen2gds.o
pgen2gds.cpp: In member function void CProgress::Reset(C_Int64):
pgen2gds.cpp:138:27: error: time was not declared in this scope
  138 |                 time_t s; time(&s);
      |                           ^~~~
pgen2gds.cpp:32:1: note: time is defined in header <ctime>; did you forget to #include <ctime>?
   31 | #include <vector>
  +++ |+#include <ctime>
   32 | 
pgen2gds.cpp: In member function void CProgress::Forward(C_Int64):
pgen2gds.cpp:162:29: error: time was not declared in this scope
  162 |                 time_t now; time(&now);
      |                             ^~~~
pgen2gds.cpp:162:29: note: time is defined in header <ctime>; did you forget to #include <ctime>?
pgen2gds.cpp:163:21: error: difftime was not declared in this scope
  163 |                 if (difftime(now, _last_check_time) > 0.25)
      |                     ^~~~~~~~
pgen2gds.cpp:163:21: note: difftime is defined in header <ctime>; did you forget to #include <ctime>?
pgen2gds.cpp: In member function void CProgress::ShowProgress():
pgen2gds.cpp:189:29: error: time was not declared in this scope
  189 |                 time_t now; time(&now);
      |                             ^~~~
pgen2gds.cpp:189:29: note: time is defined in header <ctime>; did you forget to #include <ctime>?
pgen2gds.cpp:193:35: error: difftime was not declared in this scope
  193 |                 double interval = difftime(now, _last_time);
      |                                   ^~~~~~~~
pgen2gds.cpp:193:35: note: difftime is defined in header <ctime>; did you forget to #include <ctime>?
make: *** [/home/biocbuild/bbs-3.23-bioc/R/etc/Makeconf:197: pgen2gds.o] Error 1
ERROR: compilation failed for package pgen2gds
* removing /tmp/Rtmp1R70pZ/Rinst2b5bc232740f6/pgen2gds
      -----------------------------------
ERROR: package installation failed

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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