aboutsummaryrefslogtreecommitdiff
path: root/gnu/packages/linux.scm
diff options
context:
space:
mode:
Diffstat (limited to 'gnu/packages/linux.scm')
-rw-r--r--gnu/packages/linux.scm37
1 files changed, 20 insertions, 17 deletions
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 19432817ca..3552c2e281 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -679,23 +679,26 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
#t))
(replace 'configure
(lambda* (#:key inputs native-inputs target #:allow-other-keys)
- ;; Unset CROSS_CPATH to make sure that cross-libc is not
- ;; found. Otherwise, some of its header would conflict with the
- ;; one from linux (stdint.h and linux/types.h)
- ,@(if (%current-target-system)
- '((unsetenv "CROSS_CPATH"))
- '())
-
- ;; On AArch64 (at least), we need to remove glibc headers from CPATH
- ;; (they are still available as "system headers"), so that the kernel
- ;; can override uint64_t. See <https://bugs.gnu.org/37593>.
- (setenv "CPATH"
- (string-join
- (remove (cut string-prefix? (assoc-ref inputs "libc") <>)
- (string-split (getenv "CPATH") #\:))
- ":"))
- (format #t "environment variable `CPATH' changed to `~a'~%"
- (getenv "CPATH"))
+ ;; On AArch64 (at least), we need to remove glibc headers from
+ ;; CPATH (they are still available as "system headers"), so that
+ ;; the kernel can override uint64_t. See
+ ;; <https://bugs.gnu.org/37593>. This is also true when
+ ;; cross-compiling, except in that case, cross-libc must be
+ ;; removed from CROSS_CPATH.
+ (let ((var ,(if (%current-target-system)
+ "CROSS_CPATH"
+ "CPATH"))
+ (libc ,(if (%current-target-system)
+ "cross-libc"
+ "libc")))
+ (setenv var
+ (string-join
+ (remove
+ (cut string-prefix? (assoc-ref inputs libc) <>)
+ (string-split (getenv var) #\:))
+ ":"))
+ (format #t "environment variable `~a' changed to `~a'~%"
+ var (getenv var)))
;; Avoid introducing timestamps
(setenv "KCONFIG_NOTIMESTAMP" "1")
s 2024-12-03gnu: r-spatialexperiment: Add missing inputs....* gnu/packages/bioconductor.scm (r-spatialexperiment)[native-inputs]: Add r-dropletutils. [arguments]: Add phase 'set-HOME. Change-Id: Ie08e76e22d6bf0410da2f590ac5f388f316e9111 Ricardo Wurmus 2024-12-03gnu: r-abbyyr: Add missing inputs....* gnu/packages/cran.scm (r-abbyyr)[native-inputs]: Add r-knitr and r-testthat. Change-Id: I22f32e7ea4f3aee0e4a8d1ba486495ea22789e0e Ricardo Wurmus 2024-12-03gnu: r-psupertime: Add missing input....* gnu/packages/bioinformatics.scm (r-psupertime)[native-inputs]: Add r-testthat. Change-Id: I9993547e2e757b4218c2229495a7eaa0c8fecbe2 Ricardo Wurmus 2024-12-03gnu: r-demuxmix: Add missing input....* gnu/packages/bioinformatics.scm (r-demuxmix)[native-inputs]: Add r-testthat. Change-Id: Ia09b929b4d5bb521d58fb74f17f1ac91a4d44a60 Ricardo Wurmus 2024-12-03gnu: r-cmdstanr: Add missing input....* gnu/packages/bioinformatics.scm (r-cmdstanr)[native-inputs]: Add r-testthat. Change-Id: Idd81b903e9e9a8308703c9ee8dc5583a04854678 Ricardo Wurmus 2024-12-03gnu: r-asset: Add missing input....* gnu/packages/bioconductor.scm (r-asset)[native-inputs]: Add r-biocgenerics. Change-Id: Iecfe6093665033d41b43d0ead6fa9d3f3fd54d81 Ricardo Wurmus 2024-12-03gnu: r-savr: Disable vignettes....* gnu/packages/bioconductor.scm (r-savr)[native-inputs]: Add r-testthat. [arguments]: Disable vignettes. Change-Id: If5a5928d3f7fde5d3360184b229894d92b715d03 Ricardo Wurmus 2024-12-03gnu: r-lemon: Add missing input....* gnu/packages/cran.scm (r-lemon)[native-inputs]: Add r-vdiffr. Change-Id: If7cf93031ea6a97176d7c39751aa8d6fd0858ca5 Ricardo Wurmus 2024-12-03gnu: r-sqldf: Add missing input....* gnu/packages/cran.scm (r-sqldf)[native-inputs]: Add r-svunit. Change-Id: Id62cb9aec38c547ca08f0b9ca57c190d68ef232f Ricardo Wurmus 2024-12-03gnu: r-regioner: Add missing input....* gnu/packages/bioconductor.scm (r-regioner)[native-inputs]: Add r-biocmanager. [arguments]: Add phase 'delete-bad-tests. Change-Id: I452297d9b7c776624e54bec376ed14efe4521d55 Ricardo Wurmus 2024-12-03gnu: r-biotmle: Disable tests....* gnu/packages/bioconductor.scm (r-biotmle)[native-inputs]: Add r-biotmledata. [arguments]: Disable tests. Change-Id: Ia854a6278055a2617db62cbe360b8e108e5584c7 Ricardo Wurmus 2024-12-03gnu: Add r-biotmledata....* gnu/packages/bioconductor.scm (r-biotmledata): New variable. Change-Id: If0793889ddf09b31333c8331cc5ad87f72c16ac2 Ricardo Wurmus 2024-12-03gnu: r-qdnaseq: Add missing input....* gnu/packages/bioconductor.scm (r-qdnaseq)[native-inputs]: Add r-biocstyle. Change-Id: I6a22fb4208122c5f1a6c50421129722e5b98e11d Ricardo Wurmus 2024-12-03gnu: r-motifmatchr: Add missing inputs....* gnu/packages/bioconductor.scm (r-motifmatchr)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg19. Change-Id: I90b4c258c9685047287e1e5eedbdbe9b9ce26f8f Ricardo Wurmus 2024-12-03gnu: r-glmgampoi: Add missing inputs....* gnu/packages/bioconductor.scm (r-glmgampoi)[native-inputs]: Add r-biocparallel, r-limma, r-mass, r-scran, and r-zoo. Change-Id: I5019e1b6efdad8c98245bef7512265b2141f78c9 Ricardo Wurmus 2024-12-03gnu: r-activedriverwgs: Add missing input....* gnu/packages/bioconductor.scm (r-activedriverwgs)[native-inputs]: Add r-testthat. Change-Id: Ieb45284d6a240bc88081da0018a7163a66e78b22 Ricardo Wurmus 2024-12-03gnu: r-refgenome: Disable tests....* gnu/packages/cran.scm (r-refgenome)[arguments]: Disable tests. Change-Id: I950bdf4463485fb1880934da096915ad50f3ae9e Ricardo Wurmus 2024-12-03gnu: r-sictools: Disable tests....* gnu/packages/bioconductor.scm (r-sictools)[arguments]: Disable tests. Change-Id: Id692ec7c7d5dcb17628fe818b7d116e9261ad60f Ricardo Wurmus 2024-12-03gnu: r-ffbase: Add missing inputs....* gnu/packages/cran.scm (r-ffbase)[native-inputs]: Add r-laf and r-testthat. Change-Id: I6e7e84d823e4bf4467829a78bbe8b77e26f25b8d Ricardo Wurmus 2024-12-03gnu: r-gutils: Add missing input....* gnu/packages/bioinformatics.scm (r-gutils)[native-inputs]: Add r-testthat. Change-Id: I1b5e34441b48bc92bff6538378d2e2bbc7111631 Ricardo Wurmus 2024-12-03gnu: Add r-laf....* gnu/packages/cran.scm (r-laf): New variable. Change-Id: I666b904506a929bd6bfac6782d1f4f489282ae84 Ricardo Wurmus 2024-12-03gnu: r-bamsignals: Add missing inputs....* gnu/packages/bioconductor.scm (r-bamsignals)[native-inputs]: Add r-rsamtools. Change-Id: Ifdca0e50c90349ba4179f80ea1fed91cd9ba37db Ricardo Wurmus 2024-12-03gnu: r-biocthis: Disable tests....* gnu/packages/bioconductor.scm (r-biocthis)[arguments]: Disable tests. Change-Id: Icd1a846013a36c3c8555bdcb2d6ba7dce6a8e09c Ricardo Wurmus 2024-12-03gnu: r-rticles: Add missing inputs....* gnu/packages/cran.scm (r-rticles)[native-inputs]: Add r-testthat and r-withr. Change-Id: Ia5776a0f08623f79fee2f9a9a3d2a6eeb45c9ded Ricardo Wurmus 2024-12-03gnu: r-rsconnect: Add missing input....* gnu/packages/cran.scm (r-rsconnect)[native-inputs]: Add tzdata-for-tests. Change-Id: I3bf6ef36aa5e8737aa17ce74c9141b5e784fa6df Ricardo Wurmus 2024-12-03gnu: r-visnetwork: Disable tests....* gnu/packages/cran.scm (r-visnetwork)[arguments]: Disable tests. Change-Id: I8eb926630ff35dcf6833f6dca73b54e58d84700f Ricardo Wurmus 2024-12-03gnu: r-mi: Add missing inputs....* gnu/packages/cran.scm (r-mi)[native-inputs]: Add r-betareg, r-survival, and r-truncnorm. Change-Id: I79350494404965b3f1b610dafcd1e05f3fc0c02f Ricardo Wurmus 2024-12-03gnu: r-spectra: Disable tests....* gnu/packages/bioconductor.scm (r-spectra)[arguments]: Disable tests. [native-inputs]: Add missing inputs r-mzr and r-patrick. Change-Id: I7d9dca3c1f17c0a57d7b6cc7479e08ea5bb11843 Ricardo Wurmus 2024-12-03gnu: Add r-betareg....* gnu/packages/cran.scm (r-betareg): New variable. Change-Id: I67839c22e6374dcd9e9f0c12d08770d8103ead6d Ricardo Wurmus 2024-12-03gnu: r-powertcr: Add missing input....* gnu/packages/bioconductor.scm (r-powertcr)[native-inputs]: Add r-biocgenerics. Change-Id: Ieb0f7f2bd4362a9f1d6c4a0b9b937e8be81b7323 Ricardo Wurmus 2024-12-03gnu: r-freetypeharfbuzz: Disable tests....* gnu/packages/cran.scm (r-freetypeharfbuzz)[arguments]: Disable tests. [native-inputs]: Add r-testthat. Change-Id: Ibd82aacff87c79b2c3f061035b14bb750fcee239 Ricardo Wurmus 2024-12-03gnu: r-mzr: Add missing inputs....* gnu/packages/bioconductor.scm (r-mzr)[native-inputs]: Add r-codetools, r-msdata, r-mzid, and r-xml. Change-Id: Iaeb8286a19ddb1bc750710a0e5d5a5cee59b3901 Ricardo Wurmus 2024-12-03gnu: r-depmixs4: Add missing input....* gnu/packages/cran.scm (r-depmixs4)[native-inputs]: Add r-gamlss. Change-Id: Ib7f2ab4f656bda824f2375d0d3ea59908ad1aa5c Ricardo Wurmus 2024-12-03gnu: r-sanssouci: Add missing inputs....* gnu/packages/bioconductor.scm (r-sanssouci)[native-inputs]: Add r-ggplot2 and r-testthat. [arguments]: Add phase 'delete-bad-tests. Change-Id: I902b4e4a2163f5ed9cf07d186dfe80068a8ef4a5 Ricardo Wurmus 2024-12-03gnu: r-unigd: Add missing input....* gnu/packages/cran.scm (r-unigd)[native-inputs]: Add r-xml2. Change-Id: Ice50673f8092cf37b2e26bc47bd2b1040e5e652a Ricardo Wurmus