Matthew N. McCall
| Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/frma |
| git_branch: devel |
| git_last_commit: 06e0f3f |
| git_last_commit_date: 2025-10-29 10:04:08 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 793/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| frma 1.63.0 (landing page) Matthew N. McCall
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
| See other builds for frma in R Universe. | ||||||||||||||
|
To the developers/maintainers of the frma package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/frma.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: frma |
| Version: 1.63.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:frma.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings frma_1.63.0.tar.gz |
| StartedAt: 2026-04-17 04:00:41 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 04:05:20 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 278.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: frma.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:frma.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings frma_1.63.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/frma.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘frma/DESCRIPTION’ ... OK
* this is package ‘frma’ version ‘1.63.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘frma’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’
A package should be listed in only one of these fields.
* 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 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
GNUSE: no visible binding for global variable ‘median’
GNUSE: no visible binding for global variable ‘quantile’
GNUSE: no visible global function definition for ‘boxplot’
barcode: no visible global function definition for ‘pnorm’
batchFit: no visible global function definition for ‘median’
randomeffects<-,frmaExpressionSet: no visible global function
definition for ‘validObject’
residuals<-,frmaExpressionSet: no visible global function definition
for ‘validObject’
se.exprs<-,ExpressionSet: no visible global function definition for
‘validObject’
se.exprs<-,frmaExpressionSet: no visible global function definition for
‘validObject’
weights<-,frmaExpressionSet: no visible global function definition for
‘validObject’
Undefined global functions or variables:
boxplot median pnorm quantile validObject
Consider adding
importFrom("graphics", "boxplot")
importFrom("methods", "validObject")
importFrom("stats", "median", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) frma.Rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) frma.Rd:20: Escaped LaTeX specials: \_ \_ \_
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘frma-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GNUSE
> ### Title: GNUSE
> ### Aliases: GNUSE
> ### Keywords: manip
>
> ### ** Examples
>
> library(frma)
> library(frmaExampleData)
> data(AffyBatchExample)
> object <- frma(AffyBatchExample)
also installing the dependencies ‘sys’, ‘askpass’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘httr’, ‘png’, ‘KEGGREST’, ‘AnnotationDbi’
trying URL 'https://cloud.r-project.org/src/contrib/sys_3.4.3.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/askpass_1.2.1.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/curl_7.0.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_2.0.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/mime_0.13.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/openssl_2.4.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/R6_2.6.1.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.8.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/png_0.1-9.tar.gz'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/KEGGREST_1.50.0.tar.gz'
trying URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/AnnotationDbi_1.72.0.tar.gz'
trying URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz'
* installing *source* package ‘sys’ ...
** this is package ‘sys’ version ‘3.4.3’
** package ‘sys’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c exec.c -o exec.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c init.c -o init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o sys.so exec.o init.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/00LOCK-sys/00new/sys/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (sys)
* installing *source* package ‘curl’ ...
** this is package ‘curl’ version ‘7.0.0’
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c callbacks.c -o callbacks.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c curl.c -o curl.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c download.c -o download.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c dryrun.c -o dryrun.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c escape.c -o escape.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c fetch.c -o fetch.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c findport.c -o findport.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c form.c -o form.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c getdate.c -o getdate.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c handle.c -o handle.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c ieproxy.c -o ieproxy.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c init.c -o init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c interrupt.c -o interrupt.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c multi.c -o multi.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c nslookup.c -o nslookup.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c options.c -o options.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c reflist.c -o reflist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c split.c -o split.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c ssl.c -o ssl.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c typechecking.c -o typechecking.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c urlparser.c -o urlparser.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c version.c -o version.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c winidn.c -o winidn.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c writer.c -o writer.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o dryrun.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o urlparser.o utils.o version.o winidn.o writer.o -lcurl -L/home/biocbuild/R/R/lib -lR
/usr/bin/ld: cannot find -lcurl: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/home/biocbuild/R/R/share/make/shlib.mk:10: curl.so] Error 1
ERROR: compilation failed for package ‘curl’
* removing ‘/home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/curl’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘jsonlite’ ...
** this is package ‘jsonlite’ version ‘2.0.0’
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c base64.c -o base64.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c collapse_array.c -o collapse_array.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c collapse_object.c -o collapse_object.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c collapse_pretty.c -o collapse_pretty.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c escape_chars.c -o escape_chars.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c integer64_to_na.c -o integer64_to_na.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c is_datelist.c -o is_datelist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c is_recordlist.c -o is_recordlist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c is_scalarlist.c -o is_scalarlist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c modp_numtoa.c -o modp_numtoa.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c null_to_na.c -o null_to_na.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c num_to_char.c -o num_to_char.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c parse.c -o parse.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c prettify.c -o prettify.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c push_parser.c -o push_parser.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c r-base64.c -o r-base64.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c register.c -o register.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c row_collapse.c -o row_collapse.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c transpose_list.c -o transpose_list.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c validate.c -o validate.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c yajl/yajl.c -o yajl/yajl.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c yajl/yajl_buf.c -o yajl/yajl_buf.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c yajl/yajl_encode.c -o yajl/yajl_encode.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c yajl/yajl_gen.c -o yajl/yajl_gen.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c yajl/yajl_lex.c -o yajl/yajl_lex.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c yajl/yajl_parser.c -o yajl/yajl_parser.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -Iyajl/api -I/usr/local/include -fvisibility=hidden -fPIC -g -O2 -Wall -Werror=format-security -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/00LOCK-jsonlite/00new/jsonlite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime”
in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms”
in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json”
in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64”
in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist”
in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob”
in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar”
in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf”
in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc”
in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr”
** 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 (jsonlite)
* installing *source* package ‘mime’ ...
** this is package ‘mime’ version ‘0.13’
** package ‘mime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c init.c -o init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rawmatch.c -o rawmatch.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/00LOCK-mime/00new/mime/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (mime)
* installing *source* package ‘R6’ ...
** this is package ‘R6’ version ‘2.6.1’
** package ‘R6’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R6)
* installing *source* package ‘png’ ...
** this is package ‘png’ version ‘0.1-9’
** package ‘png’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fPIC -g -O2 -Wall -Werror=format-security -c dummy.c -o dummy.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fPIC -g -O2 -Wall -Werror=format-security -c read.c -o read.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fPIC -g -O2 -Wall -Werror=format-security -c write.c -o write.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o png.so dummy.o read.o write.o -L/usr/lib64 -lpng16 -lm -lz -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/00LOCK-png/00new/png/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (png)
* installing *source* package ‘askpass’ ...
** this is package ‘askpass’ version ‘1.2.1’
** package ‘askpass’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c askpass.c -o askpass.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/00LOCK-askpass/00new/askpass/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (askpass)
* installing *source* package ‘openssl’ ...
** this is package ‘openssl’ version ‘2.4.0’
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c aes.c -o aes.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c base64.c -o base64.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bignum.c -o bignum.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cert.c -o cert.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c compatibility.c -o compatibility.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c diffie.c -o diffie.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c envelope.c -o envelope.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c error.c -o error.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c hash.c -o hash.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c info.c -o info.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c keygen.c -o keygen.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c keys.c -o keys.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c onload.c -o onload.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c openssh.c -o openssh.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c password.c -o password.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pbkdf.c -o pbkdf.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pem.c -o pem.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pkcs12.c -o pkcs12.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pkcs7.c -o pkcs7.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rand.c -o rand.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rsa.c -o rsa.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c signing.c -o signing.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ssl.c -o ssl.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c stream.c -o stream.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c write.c -o write.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c x25519.c -o x25519.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -DOPENSSL_API_COMPAT=0x10101000L -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bcrypt/blowfish.c -o bcrypt/blowfish.o
ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/00LOCK-openssl/00new/openssl/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 (openssl)
ERROR: dependency ‘curl’ is not available for package ‘httr’
Perhaps try a variation of:
install.packages('curl')
* removing ‘/home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/httr’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘httr’ had non-zero exit status
ERROR: dependency ‘httr’ is not available for package ‘KEGGREST’
Perhaps try a variation of:
install.packages('httr')
* removing ‘/home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/KEGGREST’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘KEGGREST’ had non-zero exit status
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
Perhaps try a variation of:
install.packages('KEGGREST')
* removing ‘/home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu133acdf’
Perhaps try a variation of:
install.packages('AnnotationDbi')
* removing ‘/home/biocbuild/tmp/RtmpwDjvcE/RLIBS_19f60a146c7e72/hgu133acdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘hgu133acdf’ had non-zero exit status
The downloaded source packages are in
‘/home/biocbuild/tmp/RtmpPNiuWP/downloaded_packages’
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG-U133A
Library - package hgu133acdf not installed
Library - package hgu133acdf not installed
Calls: frma ... rma.background.correct -> pm -> pm -> .local -> getCdfInfo
Execution halted
* 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 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/frma.Rcheck/00check.log’
for details.
frma.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL frma ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘frma’ ... ** this is package ‘frma’ version ‘1.63.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (frma)
frma.Rcheck/frma-Ex.timings
| name | user | system | elapsed |