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authorPjotr Prins2017-12-18 10:34:26 -0600
committerPjotr Prins2017-12-18 10:34:26 -0600
commita2a200402b91a352dbdede01eec85accb892b8e1 (patch)
tree0d70c5f83424745006ac54d405176188729b6787
parent02faf6897366c25047dbc57836a43fe5fc63ecf3 (diff)
downloadguix-bioinformatics-a2a200402b91a352dbdede01eec85accb892b8e1.tar.gz
Fixes against guix latest
-rw-r--r--gn/packages/bioinformatics.scm1
-rw-r--r--gn/packages/cwl.scm1
-rw-r--r--gn/packages/gemma.scm2
-rw-r--r--gn/packages/genenetwork.scm2
-rw-r--r--gn/packages/ldc.scm1
-rw-r--r--gn/packages/python.scm5
-rw-r--r--gn/packages/yaj.scm2
7 files changed, 11 insertions, 3 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 56ff4ab..0285b23 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -29,7 +29,6 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
#:use-module (gnu packages datastructures)
- #:use-module (gnu packages check)
#:use-module (gnu packages file)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index eed6b18..4f04f41 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -4,6 +4,7 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-web)
#:use-module (gnu packages rdf)
#:use-module (gn packages python)
#:use-module (guix download)
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 683ac46..05010a8 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -98,7 +98,7 @@
(cond
((or (string-prefix? "x86_64" system)
(string-prefix? "i686" system))
- '("DYNAMIC_ARCH=1 BINARY=64 NO_WARMUP=0 GEMM_MULTITHREAD_THRESHOLD=4 USE_THREAD=1 NO_AFFINITY=0 NO_LAPACK=1 NUM_THREADS=64"))
+ '("BINARY=64 @@ NO_WARMUP=0 GEMM_MULTITHREAD_THRESHOLD=4 USE_THREAD=1 NO_AFFINITY=0 NO_LAPACK=1 NUM_THREADS=64"))
;; On MIPS we force the "SICORTEX" TARGET, as for the other
;; two available MIPS targets special extended instructions
;; for Loongson cores are used.
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index b615f51..fa6fac0 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -35,7 +35,9 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
+ #:use-module (gnu packages python-crypto)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-web)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
diff --git a/gn/packages/ldc.scm b/gn/packages/ldc.scm
index 92406a2..835550a 100644
--- a/gn/packages/ldc.scm
+++ b/gn/packages/ldc.scm
@@ -26,6 +26,7 @@
#:use-module (guix build-system cmake)
#:use-module (gnu packages)
#:use-module (gnu packages base)
+ #:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages gdb)
#:use-module ((gnu packages ldc) #:prefix ldcmain:)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index e3f0e7a..34d0134 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -3,6 +3,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages attr)
#:use-module (gnu packages base)
+ #:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
#:use-module (gnu packages fontutils)
@@ -23,11 +24,13 @@
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-web)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages readline)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tex)
#:use-module (gnu packages texinfo)
+ #:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
@@ -128,7 +131,7 @@ functions.")
(license license:expat))
)
-(define-public python2-flask-sqlalchemy ; guix?
+(define-public python2-flask-sqlalchemy
(package-with-python2 python-flask-sqlalchemy))
(define-public python-xlsxwriter ; guix ready
diff --git a/gn/packages/yaj.scm b/gn/packages/yaj.scm
index c446e91..c5fe7fb 100644
--- a/gn/packages/yaj.scm
+++ b/gn/packages/yaj.scm
@@ -33,6 +33,8 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-web)
+ #:use-module (gnu packages check)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)