diff --git a/R/jqr.md b/R/jqr.md index 34b065d..a03214d 100644 --- a/R/jqr.md +++ b/R/jqr.md @@ -72,7 +72,7 @@ rm jqr_* This mirrors efforts above. ```bash -# download.packages("jqr",".") +# Rscript -e 'download.packages("jqr",".")' tar xvfz jqr_1.3.3.tar.gz cd jqr mv configure configure.sav diff --git a/R/magick.md b/R/magick.md index daf58c4..299cd64 100644 --- a/R/magick.md +++ b/R/magick.md @@ -6,6 +6,8 @@ sort: 12 > The magick package provide a modern and simple toolkit for image processing in R. It wraps the ImageMagick STL which is the most comprehensive open-source image processing library available today. +## 2.7.1 + When installing the package we have error message, ``` @@ -60,3 +62,28 @@ it turned out that the required ImageMick needs to be loaded as follows, ```bash module load image-magick-7.0.5-9-gcc-5.4.0-d4lemcc ``` + +## 2.8.3 + +It turned out gcc/6 is required for module `image-magick-7.0.5-9-gcc-5.4.0-d4lemcc`, coupling with C++11 via ~/.R/Makevars. + +``` +CC=gcc +CXX=g++ -std=gnu++11 +PKG_CXXFLAGS= -std=c++11 +CFLAGS = -std=c99 -I/usr/include -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -Wimplicit-function-declaration +CXXFLAGS = -std=c++11 +``` + +The setup is appropriate for module `ceuadmin/ImageMagick/7.1.1-31` with `src/Makevars` and a disabled `configure`, + +``` +PKG_CPPFLAGS=-fopenmp -DMAGICKCORE_HDRI_ENABLE=1 -DMAGICKCORE_QUANTUM_DEPTH=16 -DMAGICKCORE_CHANNEL_MASK_DEPTH=32 -I/usr/local/Cluster-Apps/ceuadmin/ImageMagick/7.1.1-31/include/ImageMagick-7 +PKG_CXXFLAGS=$(C_VISIBILITY) +PKG_LIBS=-L/usr/local/Cluster-Apps/ceuadmin/ImageMagick/7.1.1-31/lib -lm -lMagick++-7.Q16HDRI -lMagickWand-7.Q16HDRI -lMagickCore-7.Q16HDRI + +all: + +clean: + rm -f $(SHLIB) $(OBJECTS) +``` diff --git a/systems/ceuadmin.md b/systems/ceuadmin.md index 02e0ed5..3ea47d1 100644 --- a/systems/ceuadmin.md +++ b/systems/ceuadmin.md @@ -8,7 +8,7 @@ The CEU software repository is here, **/usr/local/Cluster-Apps/ceuadmin/**. ![ceuadmin](ceuadmin.png) -noting that the importance of software is purely random according to $$Poisson(N,\lambda)$$ where $$N=223$$, $$\lambda=3$$. +noting that the importance of software is purely random according to $$Poisson(N,\lambda)$$ where $$N=225$$, $$\lambda=3$$. ## Entries @@ -37,40 +37,41 @@ The current list is as follows, [77] "googletest" "graphene" "GraphicsMagick" "GreenAlgorithms4HPC" [81] "gsl" "gtk+" "gtksourceview" "gtool" [85] "hpg" "htslib" "hunspell" "icu" - [89] "ImageJ" "impute" "JabRef" "JAGS" - [93] "jq" "json-c" "KentUtils" "KING" - [97] "krb5" "lapack" "ldc2" "ldsc" -[101] "LDstore" "LEMMA" "libcares" "libgit2" -[105] "libglvnd" "libiconv" "libidn2" "libntlm" -[109] "libpng" "libseccomp" "libsodium" "libssh" -[113] "libssh2" "libuv" "libxml2" "libxslt" -[117] "locuszoom" "LVM2" "MAGENTA" "magma" -[121] "Mango" "Mega2" "metal" "MONSTER" -[125] "MORGAN" "MR-MEGA" "MsCAVIAR" "nano" -[129] "ncbi-vdb" "ncurses" "netbeans" "nettle" -[133] "nextflow" "NLopt" "node" "nspr" -[137] "oniguruma" "openjdk" "OpenMS" "openssh" -[141] "openssl" "osca" "PAINTOR" "pandoc" -[145] "pandoc-citeproc" "pango" "parallel" "Pascal" -[149] "pcre2" "pdf2djvu" "pdfjam" "peer" -[153] "pgsc_calc" "phenoscanner" "PhySO" "picard" -[157] "plink" "plink-bgi" "plinkseq" "PoGo" -[161] "polyphen" "poppler" "popt" "proj" -[165] "PRSice" "pspp" "pulsar" "PWCoCo" -[169] "qctool" "qpdf" "qt" "qtcreator" -[173] "QTLtools" "quarto" "quicktest" "R" -[177] "raremetal" "rclone" "readline" "regenie" -[181] "regtools" "RHHsoftware" "rst2pdf" "rstudio" -[185] "ruby" "rust" "samtools" "Scala" -[189] "shapeit" "singularity" "SMR" "snakemake" -[193] "SNP2HLA" "snptest" "spread-sheet-widget" "sqlite" -[197] "sra-tools" "ssw" "STAR" "stata" -[201] "SurvivalAnalysis" "SurvivalKit" "Swift" "tabix" -[205] "tatami" "thunderbird" "tidy" "trinculo" -[209] "trousers" "Typora" "unbound" "vala" -[213] "VarScan" "vcftools" "VEGAS2" "verifyBamID" -[217] "VSCode" "VSCodium" "vte" "xpdf" -[221] "yaml-cpp" "Zotero" "zstd" + [89] "ImageJ" "ImageMagick" "impute" "JabRef" + [93] "JAGS" "jq" "json-c" "KentUtils" + [97] "KING" "krb5" "lapack" "ldc2" +[101] "ldsc" "LDstore" "LEMMA" "libcares" +[105] "libgit2" "libglvnd" "libiconv" "libidn2" +[109] "libntlm" "libpng" "libseccomp" "libsodium" +[113] "libssh" "libssh2" "libuv" "libxml2" +[117] "libxslt" "locuszoom" "LVM2" "MAGENTA" +[121] "magma" "Mango" "Mega2" "metal" +[125] "MONSTER" "MORGAN" "MR-MEGA" "MsCAVIAR" +[129] "nano" "ncbi-vdb" "ncurses" "netbeans" +[133] "nettle" "nextflow" "nlopt" "NLopt" +[137] "node" "nspr" "oniguruma" "openjdk" +[141] "OpenMS" "openssh" "openssl" "osca" +[145] "PAINTOR" "pandoc" "pandoc-citeproc" "pango" +[149] "parallel" "Pascal" "pcre2" "pdf2djvu" +[153] "pdfjam" "peer" "pgsc_calc" "phenoscanner" +[157] "PhySO" "picard" "plink" "plink-bgi" +[161] "plinkseq" "PoGo" "polyphen" "poppler" +[165] "popt" "proj" "PRSice" "pspp" +[169] "pulsar" "PWCoCo" "qctool" "qpdf" +[173] "qt" "qtcreator" "QTLtools" "quarto" +[177] "quicktest" "R" "raremetal" "rclone" +[181] "readline" "regenie" "regtools" "RHHsoftware" +[185] "rst2pdf" "rstudio" "ruby" "rust" +[189] "samtools" "Scala" "shapeit" "singularity" +[193] "SMR" "snakemake" "SNP2HLA" "snptest" +[197] "spread-sheet-widget" "sqlite" "sra-tools" "ssw" +[201] "STAR" "stata" "SurvivalAnalysis" "SurvivalKit" +[205] "Swift" "tabix" "tatami" "thunderbird" +[209] "tidy" "trinculo" "trousers" "Typora" +[213] "unbound" "vala" "VarScan" "vcftools" +[217] "VEGAS2" "verifyBamID" "VSCode" "VSCodium" +[221] "vte" "xpdf" "yaml-cpp" "Zotero" +[225] "zstd" ``` These are wrapped up as :star::star::star: **[modules](https://modules.readthedocs.io/en/latest/index.html)** :star::star::star:. diff --git a/systems/ceuadmin.png b/systems/ceuadmin.png index c5a83d3..a54e3cc 100644 Binary files a/systems/ceuadmin.png and b/systems/ceuadmin.png differ diff --git a/systems/generic.png b/systems/generic.png index cb6e19c..bd6e06a 100644 Binary files a/systems/generic.png and b/systems/generic.png differ diff --git a/systems/genetics.png b/systems/genetics.png index 5d1295d..87d26a4 100644 Binary files a/systems/genetics.png and b/systems/genetics.png differ diff --git a/systems/setup.md b/systems/setup.md index 1e7b93f..5aeb548 100644 --- a/systems/setup.md +++ b/systems/setup.md @@ -268,6 +268,7 @@ All entries are ordered chronologically. ! "" | libssh2/1.11.0-icelake | Generic | ! "" | libssh/0.10.6-icelake | Generic | ! 2024-04-22 | peer/1.3 | Generic[^peer] | +! 2024-04-29 | ImageMagick/7.1.1-31 | Generic[^ImageMagick]| \* CEU or approved users only. @@ -285,7 +286,7 @@ They are generated from the following script, if [ "$(uname -n | sed 's/-[0-9]*$//')" == "login-p" ]; then module load ceuadmin/R else - module load ceuadmin/R/4.3.3-icelake + module load ceuadmin/R/4.4.0-icelake fi grep -e Generic ${CEUADMIN}/doc/setup.md | grep "^[|]" | awk '{print $4}' > generic.lst grep -e Genetics ${CEUADMIN}/doc/setup.md | grep "^[|]" | awk '{print $4}' > genetics.lst @@ -904,3 +905,14 @@ Rscript -e ' [^peer]: **peer** This is documented separately in the R section, . + +[^ImageMagick]: **ImageMagick** + + ```bash + wget -qO- https://github.com/ImageMagick/ImageMagick/archive/refs/tags/7.1.1-31.tar.gz | \ + tar xvfz - + cd ImageMagick-7.1.1-31/ + ./configure --prefix=$CEUADMIN/ImageMagick/7.1.1-31 + make + make install + ```