Install package

[vkummer]

Hi, I wanted to install the package using devtools::install_github("dselivanov/rsparse") but the installation always fails. The error it shows is:

ERROR: dependency ‘float’ is not available for package ‘rsparse’

How can I fix this?

[dselivanov]

Try devtools::install_github("dselivanov/float") and then install rsparse. ср, 25 апр. 2018 г., 9:30 vkummer <notifications@github.com>:

…

Hi, I wanted to install the package using devtools::install_github("dselivanov/rsparse") but the installation always fails. The error it shows is: ERROR: dependency ‘float’ is not available for package ‘rsparse’ How can I fix this? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE4u3RfF5QFDyv7kn1PLkFMfc04WOAMLks5tsHqOgaJpZM4Tjbau> .

[vkummer]

Thank you for your prompt reply. Couldn't install float though, here are the error messages I get:

ERROR: configuration failed for package ‘float’

C compiler cannot create executables

[dselivanov]

Not sure why. Please provide `sessionInfo` and configure installation log. ср, 25 апр. 2018 г., 9:54 vkummer <notifications@github.com>:

…

Thank you for your prompt reply. Couldn't install float though, here are the error messages I get: ERROR: configuration failed for package ‘float’ C compiler cannot create executables — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE4u3Vu9wyY4iDS0ejJCwi42XqWoxbrQks5tsIAGgaJpZM4Tjbau> .

[dselivanov]

`sessionInfo()` call :-) ср, 25 апр. 2018 г., 10:11 vkummer <notifications@github.com>:

…

sessionInfo function (package = NULL) { z <- list() z$R.version <- R.Version() z$platform <- z$R.version$platform if (nzchar(.Platform$r_arch)) z$platform <- paste(z$platform, .Platform$r_arch, sep = "/") z$platform <- paste0(z$platform, " (", 8 * .Machine$sizeof.pointer, "-bit)") z$locale <- Sys.getlocale() if (.Platform$OS.type == "windows") { z$running <- win.version() } else if (nzchar(Sys.which("uname"))) { uname <- system("uname -a", intern = TRUE) os <- sub(" . *", "", uname) z$running <- switch(os, Linux = if (file.exists("/etc/os-release")) { tmp <- readLines("/etc/os-release") t2 <- if (any(startsWith(tmp, "PRETTY_NAME="))) sub("^PRETTY_NAME=", "", grep("^PRETTY_NAME=", tmp, value = TRUE)[1L]) else if (any(startsWith(tmp, "NAME"))) sub("^NAME=", "", grep("^NAME=", tmp, value = TRUE)[1L]) else "Linux (unknown distro)" sub(""(.*)"", "\1", t2) } else if (file.exists("/etc/system-release")) { readLines("/etc/system-release") }, Darwin = { ver <- readLines("/System/Library/CoreServices/SystemVersion.plist") ind <- grep("ProductUserVisibleVersion", ver) ver <- ver[ind + 1L] ver <- sub(".*", "", ver) ver <- sub("$", "", ver) ver1 <- strsplit(ver, ".", fixed = TRUE)[[1L]][2L] sprintf("%s %s %s", ifelse(as.numeric(ver1) < 12, "OS X", "macOS"), switch(ver1, 6 = "Snow Leopard", 7 = "Lion", 8 = "Mountain Lion", 9 = "Mavericks", 10 = "Yosemite", 11 = "El Capitan", 12 = "Sierra", 13 = "High Sierra", ""), ver) }, SunOS = { ver <- system("uname -r", intern = TRUE) paste("Solaris", strsplit(ver, ".", fixed = TRUE)[[1L]][2L]) }, uname) } if (is.null(package)) { package <- grep("^package:", search(), value = TRUE) keep <- vapply(package, function(x) x == "package:base" || !is.null(attr(as.environment(x), "path")), NA) package <- .rmpkg(package[keep]) } pkgDesc <- lapply(package, packageDescription, encoding = NA) if (length(package) == 0) stop("no valid packages were specified") basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && x$Priority == "base") z$basePkgs <- package[basePkgs] if (any(!basePkgs)) { z$otherPkgs <- pkgDesc[!basePkgs] names(z$otherPkgs) <- package[!basePkgs] } loadedOnly <- loadedNamespaces() loadedOnly <- loadedOnly[!(loadedOnly %in% package)] if (length(loadedOnly)) { names(loadedOnly) <- loadedOnly pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription)) z$loadedOnly <- pkgDesc[loadedOnly] } z$matprod <- as.character(options("matprod")) es <- extSoftVersion() z$BLAS <- as.character(es["BLAS"]) z$LAPACK <- La_library() class(z) <- "sessionInfo" z } <bytecode: 0x7fd6d44d6a30> <environment: namespace:utils> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE4u3bmwErgi_1E8CxbfDV8HEFV7fNIyks5tsIQqgaJpZM4Tjbau> .

[vkummer]

Oh, sorry..

sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] de_CH.UTF-8/de_CH.UTF-8/de_CH.UTF-8/C/de_CH.UTF-8/de_CH.UTF-8

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

loaded via a namespace (and not attached):
[1] httr_1.3.1 compiler_3.4.4 R6_2.2.2 tools_3.4.4
[5] withr_2.1.2 curl_3.2 memoise_1.1.0 git2r_0.21.0
[9] digest_0.6.15 devtools_1.13.5

[dselivanov]

strange - I also use R 3.4.4 on OS X. What does installation of float say? Could you provide full installation log ?

[avivbrokman]

I'd like to try out your factorization machine R code, to share with my class, but I'm also unable to install float. I am including the two things you requested from 'vkummer': the installation log and 'sessionInfo()`

FULL INSTALLATION LOG:

devtools::install_github("dselivanov/float")
Downloading GitHub repo dselivanov/float@master
from URL https://api.github.com/repos/dselivanov/float/zipball/master
Installing float
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save
--no-restore --quiet CMD INSTALL
'/private/var/folders/mc/r7wbwryj10d3lybv8ctp47ww0000gn/T/RtmpUQfk2C/devtools39a049d0ecd6/dselivanov-float-1e09d8b'
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests

• installing source package ‘float’ ...
  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 for gcc option to accept ISO C99... none needed
  checking for sinf in -lm... yes
  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 whether byte ordering is bigendian... no
  checking size of int... 4
  checking for echo... yes
  checking for grep... yes
  checking for sgemm_ in -lRblas... no
  checking for sgetrf_ in -lRblas... no
  checking for sgetrf_ in -lRlapack... no
  checking for g77... no
  checking for xlf... no
  checking for f77... no
  checking for frt... no
  checking for pgf77... no
  checking for cf77... no
  checking for fort77... no
  checking for fl32... no
  checking for af77... no
  checking for xlf90... no
  checking for f90... no
  checking for pgf90... no
  checking for pghpf... no
  checking for epcf90... no
  checking for gfortran... no
  checking for g95... no
  checking for xlf95... no
  checking for f95... no
  checking for fort... no
  checking for ifort... no
  checking for ifc... no
  checking for efc... no
  checking for pgfortran... no
  checking for pgf95... no
  checking for lf95... no
  checking for ftn... no
  checking for nagfor... no
  checking whether we are using the GNU Fortran 77 compiler... no
  checking whether accepts -g... no

******************** Results of spm package configure *******************

• using 'int' for internal float storage
• NOTE: using package's single precision blas

  BLAS_LIBS=-L/Library/Frameworks/R.framework/Resources/lib -lRblas

• NOTE: using package's single precision lapack

  LAPACK_LIBS=-L/Library/Frameworks/R.framework/Resources/lib -lRlapack

The internal single precision BLAS are inefficient. Please consider installing high performance implementations, such as OpenBLAS (open source software) or MKL (available for free from the Microsoft R Open R distribution).

If you believe you are seeing this message in error, please contact the package maintainer.

---

configure: creating ./config.status
config.status: creating src/endianness.h
configure: creating ./config.status
config.status: creating src/endianness.h
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fopenmp -I../inst/include/ -fPIC -Wall -g -O2 -c backsolve.c -o backsolve.o
clang: error: unsupported option '-fopenmp'
make: *** [backsolve.o] Error 1
ERROR: compilation failed for package ‘float’

• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/float’
  Installation failed: Command failed (1)

SESSION INFO():

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] Rcpp_0.12.16 devtools_1.13.5 mlapi_0.1.0

loaded via a namespace (and not attached):
[1] httr_1.3.1 compiler_3.4.2 R6_2.2.2 tools_3.4.2 withr_2.1.2 rstudioapi_0.7
[7] curl_3.1 memoise_1.1.0 knitr_1.17 git2r_0.21.0 digest_0.6.12

[dselivanov]

@avivbrokman please install clang with openmp support - check instructions here.

[dselivanov]

@vkummer @avivbrokman I've removed float from dependencies and made robust configure script to identify OpenMP, BLAS, LAPACK. I believe now package can be easily installed with devtools::install_github("dselivanov/rsparse"). Please try and report if this doesn't work.

[vkummer]

@dselivanov I tried to run devtools::install_github("dselivanov/rsparse") but it still doesn't work. Installation log:

devtools::install_github("dselivanov/rsparse")
Downloading GitHub repo dselivanov/rsparse@master
from URL https://api.github.com/repos/dselivanov/rsparse/zipball/master
Installing rsparse
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/kp/6kw79gtn6s54f6rz9d85ltzm0000gn/T/Rtmpn4ApQ3/devtools55964dd27359/dselivanov-rsparse-1a23602'
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'
--install-tests

• installing source package ‘rsparse’ ...
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
  checking for echo... yes
  checking for grep... yes
  checking for gcc... gcc
  checking whether the C compiler works... no
  configure: error: in /private/var/folders/kp/6kw79gtn6s54f6rz9d85ltzm0000gn/T/Rtmpn4ApQ3/devtools55964dd27359/dselivanov-rsparse-1a23602': configure: error: C compiler cannot create executables See config.log' for more details
  ERROR: configuration failed for package ‘rsparse’
• removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rsparse’
  Installation failed: Command failed (1)

[dselivanov]

In order to be be able to install packages from source you need to isntall xcode:

xcode-select --install