GerardTromp commented 10 months ago

Greetings!

Just tried to install the package (version 1.14.0) on Ubuntu 22.04 and R 4.3.1.

I received the error message:

** testing if installed package keeps a record of temporary installation path
ERROR: hard-coded installation path: please report to the package maintainer and use ‘--no-staged-install’

Herewith the report as suggested by the R install check

tgirke commented 10 months ago

I have never seen this on our systems or from users. Could you sent the commands you use for the install and the output of sessionInfo() after your run into this error.

GerardTromp commented 10 months ago

Oddly enough, the error disappeared when re-installing it now (for test purposes).

I originally installed it from the command line, and it then installed with the flag "-no-staged-install".

Today, the error did not occur.

R CMD INSTALL signatureSearch_1.14.0.tar.gz

installing to library '/usr/local/lib/R/site-library'

installing source package 'signatureSearch' ... using staged installation libs using C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' using C++ compiler: 'g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' using C++11 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fastGSEA.cpp -o fastGSEA.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fgsea_init.c -o fgsea_init.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/signatureSearch/libs 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 (signatureSearch)

If relevant, sessionInfo reports the following as the first thing (only base packages loaded).

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Africa/Johannesburg tzcode source: system (glibc)

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_4.3.1

Gerard

From: Thomas Girke @.> Sent: 2023-10-05 Thursday 16:50 To: girke-lab/signatureSearch @.> Cc: Tromp, Gerard, Prof @. @.>; Author @.***> Subject: Re: [girke-lab/signatureSearch] hard-coded installation path (Issue #17)

CAUTION: This email originated from outside the Stellenbosch University network. Do not click links or open attachments unless you recognize the sender and know the content is safe.

I have never seen this on our systems or from users. Could you sent the output of sessionInfo() after your run into this error.

- Reply to this email directly, view it on GitHubhttps://github.com/girke-lab/signatureSearch/issues/17#issuecomment-1749064886, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCBWDKQAPFSGS473S2LXYLX53CKDAVCNFSM6AAAAAA5TZZVNCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBZGA3DIOBYGY. You are receiving this because you authored the thread.Message ID: @.**@.>>

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GerardTromp commented 10 months ago

I tried the install in an R session on another server:

This time it seems the error was propagating from a dependency. Yesterday's error was not nearly as "verbose" and only seemed to be about signatureSearch. It thus appears that one of the dependencies might be throwing the error, and depending on what is already installed, it is emitted only in the signatureSearch portion.

Here it seemed like it was affyio or R.methodsS3, or both.

installing source package 'signatureSearch' ... using staged installation libs using C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' using C++ compiler: 'g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' using C++11 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fastGSEA.cpp -o fastGSEA.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fgsea_init.c -o fgsea_init.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/signatureSearch/libs R data * moving datasets to lazyload DB inst ** byte-compile and prepare package for lazy loading trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/affyio_1.70.0.tar.gz' Content type 'application/x-gzip' length 110373 bytes (107 KB)

downloaded 107 KB

x-gzip' length 384384 bytes (375 KB)

downloaded 375 KB

trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz' Content type 'application/x-gzip' length 24131 bytes (23 KB)

downloaded 23 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/affy_1.78.2.tar.gz' Content type 'application/x-gzip' length 1222237 bytes (1.2 MB)

downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.12.2.tar.gz' Content type 'application/x-gzip' length 365876 bytes (357 KB)

downloaded 357 KB

trying URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/signatureSearchData_1.14.0.tar.gz' Content type 'application/x-gzip' length 659258 bytes (643 KB)

downloaded 643 KB

installing source package 'affyio' ... using staged installation 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 how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for main in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars libs using C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fread_functions.c -o fread_functions.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init_package.c -o init_package.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_abatch.c -o read_abatch.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:698:27: warning: 'builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 698 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin_sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | va_arg_pack ()); | ~~~~~ read_bpmap.c:655:27: warning: '_builtinsprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 655 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | va_arg_pack ()); | ~~~~~ read_bpmap.c:603:25: warning: '_builtinsprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 603 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~ gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdf_xda.c -o read_cdf_xda.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdffile2.c -o read_cdffile2.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_celfile_generic.c -o read_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_clf.c -o read_clf.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_generic.c -o read_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_pgf.c -o read_pgf.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/00LOCK-affyio/00new/affyio/libs R 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 ERROR: hard-coded installation path: please report to the package maintainer and use '--no-staged-install'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/affyio' Warning in install.packages(...) : installation of package 'affyio' had non-zero exit status
installing source package 'R.methodsS3' ... package 'R.methodsS3' successfully unpacked and MD5 sums checked using staged installation 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 testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path ERROR: hard-coded installation path: please report to the package maintainer and use '--no-staged-install'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/R.methodsS3' Warning in install.packages(...) : installation of package 'R.methodsS3' had non-zero exit status ERROR: dependency 'R.methodsS3' is not available for package 'R.oo'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/R.oo' Warning in install.packages(...) : installation of package 'R.oo' had non-zero exit status ERROR: dependency 'affyio' is not available for package 'affy'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/affy' Warning in install.packages(...) : installation of package 'affy' had non-zero exit status ERROR: dependencies 'R.oo', 'R.methodsS3' are not available for package 'R.utils'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/R.utils' Warning in install.packages(...) : installation of package 'R.utils' had non-zero exit status ERROR: dependencies 'affy', 'R.utils' are not available for package 'signatureSearchData'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/signatureSearchData' Warning in install.packages(...) : installation of package 'signatureSearchData' had non-zero exit status

The downloaded source packages are in '/tmp/RtmppsjGPK/downloaded_packages' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/affyio_1.70.0.tar.gz' Content type 'application/x-gzip' length 110373 bytes (107 KB)

downloaded 107 KB

trying URL 'https://cloud.r-project.org/src/contrib/R.oo_1.25.0.tar.gz' Content type 'application/x-gzip' length 384384 bytes (375 KB)

downloaded 375 KB

trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz' Content type 'application/x-gzip' length 24131 bytes (23 KB)

downloaded 23 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/affy_1.78.2.tar.gz' Content type 'application/x-gzip' length 1222237 bytes (1.2 MB)

downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.12.2.tar.gz' Content type 'application/x-gzip' length 365876 bytes (357 KB)

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trying URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/signatureSearchData_1.14.0.tar.gz' Content type 'application/x-gzip' length 659258 bytes (643 KB)

downloaded 643 KB

installing source package 'affyio' ... using staged installation 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 how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for main in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars libs using C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fread_functions.c -o fread_functions.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init_package.c -o init_package.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_abatch.c -o read_abatch.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:698:27: warning: 'builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 698 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin_sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | va_arg_pack ()); | ~~~~~ read_bpmap.c:655:27: warning: '_builtinsprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 655 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | va_arg_pack ()); | ~~~~~ read_bpmap.c:603:25: warning: '_builtinsprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 603 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~ gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdf_xda.c -o read_cdf_xda.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdffile2.c -o read_cdffile2.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_celfile_generic.c -o read_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_clf.c -o read_clf.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_generic.c -o read_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I'/usr/local/lib/R/site-library/Rcpp/include' -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_pgf.c -o read_pgf.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/00LOCK-affyio/00new/affyio/libs R 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 ERROR: hard-coded installation path: please report to the package maintainer and use '--no-staged-install'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/affyio' Warning in install.packages(...) : installation of package 'affyio' had non-zero exit status
installing source package 'R.methodsS3' ... package 'R.methodsS3' successfully unpacked and MD5 sums checked using staged installation 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 testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path ERROR: hard-coded installation path: please report to the package maintainer and use '--no-staged-install'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/R.methodsS3' Warning in install.packages(...) : installation of package 'R.methodsS3' had non-zero exit status ERROR: dependency 'R.methodsS3' is not available for package 'R.oo'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/R.oo' Warning in install.packages(...) : installation of package 'R.oo' had non-zero exit status ERROR: dependency 'affyio' is not available for package 'affy'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/affy' Warning in install.packages(...) : installation of package 'affy' had non-zero exit status ERROR: dependencies 'R.oo', 'R.methodsS3' are not available for package 'R.utils'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/R.utils' Warning in install.packages(...) : installation of package 'R.utils' had non-zero exit status ERROR: dependencies 'affy', 'R.utils' are not available for package 'signatureSearchData'
removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/signatureSearchData' Warning in install.packages(...) : installation of package 'signatureSearchData' had non-zero exit status

The downloaded source packages are in '/tmp/RtmppsjGPK/downloaded_packages' ** 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 (signatureSearch)

The downloaded source packages are in '/tmp/RtmpTQSdAI/downloaded_packages'

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3; LAPACK version 3.10.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Africa/Johannesburg tzcode source: system (glibc)

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] BiocManager_1.30.22 compiler_4.3.1 tools_4.3.1

From: Thomas Girke @.> Sent: 2023-10-05 Thursday 16:50 To: girke-lab/signatureSearch @.> Cc: Tromp, Gerard, Prof @. @.>; Author @.***> Subject: Re: [girke-lab/signatureSearch] hard-coded installation path (Issue #17)

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I have never seen this on our systems or from users. Could you sent the output of sessionInfo() after your run into this error.

- Reply to this email directly, view it on GitHubhttps://github.com/girke-lab/signatureSearch/issues/17#issuecomment-1749064886, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCBWDKQAPFSGS473S2LXYLX53CKDAVCNFSM6AAAAAA5TZZVNCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBZGA3DIOBYGY. You are receiving this because you authored the thread.Message ID: @.**@.>>

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tgirke commented 10 months ago

I see. Since signatureSearch is a Bioconductor package, you want (need) to install it with BiocManager::install(...) as shown here. This applies to all Bioconductor packages.

tgirke commented 10 months ago

,,,

GerardTromp commented 10 months ago

Final note.

The packages that had installation errors when signatureSearch tries to install them as sub-processes, install without error when installed directly [install.packages()/BiocManager::install()].

ERROR: hard-coded installation path: please report to the package maintainer and use '--no-staged-install'

removing '/usr/local/lib/R/site-library/00LOCK-signatureSearch/00new/affyio'

Note the 00new/affyio as a subdirectory. It seems the error stems from that.

Installing affyio and the other missing packages e.g., BiocManager::install(c("affyio","affy", "R.oo", "R.utils", "signatureSearchData" ))

works correctly without error.

Limited log output

installing source package 'affyio' ... using staged installation 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 how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for main in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars libs using C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fread_functions.c -o fread_functions.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init_package.c -o init_package.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_abatch.c -o read_abatch.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function 'ReadBPMAPFileIntoRList': read_bpmap.c:698:27: warning: 'builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 698 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin_sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | va_arg_pack ()); | ~~~~~ read_bpmap.c:655:27: warning: '_builtinsprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 655 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | va_arg_pack ()); | ~~~~~ read_bpmap.c:603:25: warning: '_builtinsprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 603 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:894, from /usr/share/R/include/R.h:44, from read_bpmap.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: 'builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 10 38 | return builtin_sprintf_chk (s, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~ 39 | glibc_objsize (s), fmt, | ~~~~~~~~~ 40 | __va_arg_pack ()); | ~~~~~ gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdf_xda.c -o read_cdf_xda.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_cdffile2.c -o read_cdffile2.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_celfile_generic.c -o read_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_clf.c -o read_clf.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_generic.c -o read_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_pgf.c -o read_pgf.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-affyio/00new/affyio/libs R 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 (affyio)
installing source package 'R.oo' ... package 'R.oo' successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function getMethods to getMethods.default, which was defined in environment R.oo. Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function getClasses to getClasses.default, which was defined in environment R.oo. help * installing help indices 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 (R.oo)
installing source package 'R.utils' ... package 'R.utils' successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function warnings to warnings.default, which was defined in environment R.utils. help * installing help indices 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 (R.utils)
installing source package 'signatureSearchData' ... 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 (signatureSearchData)

It therefore is not signatureSearch per se, but rather installing dependencies as child processes that seems to trigger the error.

Gerard

From: Thomas Girke @.> Sent: 2023-10-05 Thursday 16:50 To: girke-lab/signatureSearch @.> Cc: Tromp, Gerard, Prof @. @.>; Author @.***> Subject: Re: [girke-lab/signatureSearch] hard-coded installation path (Issue #17)

CAUTION: This email originated from outside the Stellenbosch University network. Do not click links or open attachments unless you recognize the sender and know the content is safe.

I have never seen this on our systems or from users. Could you sent the output of sessionInfo() after your run into this error.

- Reply to this email directly, view it on GitHubhttps://github.com/girke-lab/signatureSearch/issues/17#issuecomment-1749064886, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCBWDKQAPFSGS473S2LXYLX53CKDAVCNFSM6AAAAAA5TZZVNCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBZGA3DIOBYGY. You are receiving this because you authored the thread.Message ID: @.**@.>>

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GerardTromp commented 10 months ago

I just sent a bunch of messages and logs from BiocManager::install.

The upshot is that the error is from the installation of dependencies as child processes from signatureSearch.

Gerard

From: Thomas Girke @.> Sent: 2023-10-05 Thursday 18:54 To: girke-lab/signatureSearch @.> Cc: Tromp, Gerard, Prof @. @.>; Author @.***> Subject: Re: [girke-lab/signatureSearch] hard-coded installation path (Issue #17)

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I see. Since signatureSearch is a Bioconductor package, you want (need) to install it with BiocManager::install(...) as shown herehttps://bioconductor.org/packages/release/bioc/html/signatureSearch.html. This applies to all Bioconductor packages.

- Reply to this email directly, view it on GitHubhttps://github.com/girke-lab/signatureSearch/issues/17#issuecomment-1749308052, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGCBWDI5NAEBUP5IOR3MJD3X53Q3XAVCNFSM6AAAAAA5TZZVNCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBZGMYDQMBVGI. You are receiving this because you authored the thread.Message ID: @.**@.>>

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girke-lab / signatureSearch

hard-coded installation path #17

trying URL 'https://cloud.r-project.org/src/contrib/R.oo_1.25.0.tar.gz' Content type 'application/x-gzip' length 384384 bytes (375 KB)

trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz' Content type 'application/x-gzip' length 24131 bytes (23 KB)

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/affy_1.78.2.tar.gz' Content type 'application/x-gzip' length 1222237 bytes (1.2 MB)

trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.12.2.tar.gz' Content type 'application/x-gzip' length 365876 bytes (357 KB)

trying URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/signatureSearchData_1.14.0.tar.gz' Content type 'application/x-gzip' length 659258 bytes (643 KB)

The downloaded source packages are in '/tmp/RtmppsjGPK/downloaded_packages' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/affyio_1.70.0.tar.gz' Content type 'application/x-gzip' length 110373 bytes (107 KB)

trying URL 'https://cloud.r-project.org/src/contrib/R.oo_1.25.0.tar.gz' Content type 'application/x-gzip' length 384384 bytes (375 KB)

trying URL 'https://cloud.r-project.org/src/contrib/R.methodsS3_1.8.2.tar.gz' Content type 'application/x-gzip' length 24131 bytes (23 KB)

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/affy_1.78.2.tar.gz' Content type 'application/x-gzip' length 1222237 bytes (1.2 MB)

trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.12.2.tar.gz' Content type 'application/x-gzip' length 365876 bytes (357 KB)

trying URL 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/signatureSearchData_1.14.0.tar.gz' Content type 'application/x-gzip' length 659258 bytes (643 KB)