Installation failed

[marzamKI]

hey there,

I am trying to install h5 but keep getting error:

Downloading GitHub repo mannau/h5@master
from URL https://api.github.com/repos/mannau/h5/zipball/master
Installing h5
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL  \
  '/private/var/folders/xk/7tdpfsld6g9143qcprkkh9sw0000gp/T/Rtmpy0JxGb/devtools10d5c5b155690/mannau-h5-09382bb'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests 

* installing *source* package ‘h5’ ...
checking for h5c++... /usr/local/bin/h5c++
checking for ggrep... /usr/bin/grep
checking whether /usr/bin/grep accepts -o... yes
checking for ggrep... (cached) /usr/bin/grep
checking whether /usr/bin/grep accepts -o... yes
configure: creating ./config.status
config.status: creating src/Makevars
Warning in as.POSIXlt.POSIXct(x, tz) :
  unknown timezone 'zone/tz/2017c.1.0/zoneinfo/Europe/Stockholm'
** libs
XX -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/hdf5/1.10.1_2/include -I/usr/local/opt/szip/include  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Attribute.cpp -o Attribute.o
/bin/sh: XX: command not found
make: *** [Attribute.o] Error 127
ERROR: compilation failed for package ‘h5’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/h5’
Installation failed: Command failed (1)

Session info:

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

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] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Seurat_2.1.0        Biobase_2.38.0      BiocGenerics_0.24.0 Matrix_1.2-12       cowplot_0.9.1      
[6] ggplot2_2.2.1      

loaded via a namespace (and not attached):
  [1] backports_1.1.1        Hmisc_4.0-3            VGAM_1.0-4             NMF_0.20.6            
  [5] sn_1.5-1               plyr_1.8.4             igraph_1.1.2           lazyeval_0.2.1        
  [9] splines_3.4.2          densityClust_0.3       fastICA_1.2-1          gridBase_0.4-7        
 [13] digest_0.6.12          foreach_1.4.3          htmltools_0.3.6        viridis_0.4.0         
 [17] lars_1.2               gdata_2.18.0           memoise_1.1.0          magrittr_1.5          
 [21] checkmate_1.8.5        cluster_2.0.6          doParallel_1.0.11      mixtools_1.1.0        
 [25] ROCR_1.0-7             sfsmisc_1.1-1          limma_3.34.3           recipes_0.1.1         
 [29] gower_0.1.2            dimRed_0.1.0           matrixStats_0.52.2     R.utils_2.6.0         
 [33] colorspace_1.3-2       ggrepel_0.7.0          dplyr_0.7.4            bindr_0.1             
 [37] survival_2.41-3        iterators_1.0.8        ape_5.0                glue_1.2.0            
 [41] DRR_0.0.2              registry_0.5           gtable_0.2.0           ipred_0.9-6           
 [45] kernlab_0.9-25         ddalpha_1.3.1          prabclus_2.2-6         DEoptimR_1.0-8        
 [49] scales_0.5.0           pheatmap_1.0.8         mvtnorm_1.0-6          rngtools_1.2.4        
 [53] Rcpp_0.12.14           dtw_1.18-1             viridisLite_0.2.0      xtable_1.8-2          
 [57] htmlTable_1.11.0       tclust_1.3-1           foreign_0.8-69         proxy_0.4-19          
 [61] mclust_5.4             SDMTools_1.1-221       Formula_1.2-2          tsne_0.1-3            
 [65] stats4_3.4.2           lava_1.5.1             prodlim_1.6.1          httr_1.3.1            
 [69] htmlwidgets_0.9        FNN_1.1                gplots_3.0.1           RColorBrewer_1.1-2    
 [73] fpc_2.1-10             acepack_1.4.1          modeltools_0.2-21      ica_1.0-1             
 [77] pkgconfig_2.0.1        R.methodsS3_1.7.1      flexmix_2.3-14         nnet_7.3-12           
 [81] caret_6.0-77           tidyselect_0.2.3       rlang_0.1.4            reshape2_1.4.2        
 [85] munsell_0.4.3          tools_3.4.2            ranger_0.8.0           devtools_1.13.4       
 [89] ggridges_0.4.1         broom_0.4.3            stringr_1.2.0          yaml_2.1.15           
 [93] ModelMetrics_1.1.0     knitr_1.17             robustbase_0.92-8      caTools_1.17.1        
 [97] DDRTree_0.1.5          purrr_0.2.4            RANN_2.5.1             bindrcpp_0.2          
[101] pbapply_1.3-3          nlme_3.1-131           monocle_2.6.1          slam_0.1-40           
[105] R.oo_1.21.0            RcppRoll_0.2.2         compiler_3.4.2         rstudioapi_0.7        
[109] curl_3.0               ggjoy_0.4.0            tibble_1.3.4           stringi_1.1.6         
[113] lattice_0.20-35        trimcluster_0.1-2      psych_1.7.8            HSMMSingleCell_0.112.0
[117] diffusionMap_1.1-0     combinat_0.0-8         data.table_1.10.4-3    bitops_1.0-6          
[121] irlba_2.3.2            R6_2.2.2               latticeExtra_0.6-28    KernSmooth_2.23-15    
[125] gridExtra_2.3          codetools_0.2-15       MASS_7.3-47            gtools_3.5.0          
[129] assertthat_0.2.0       CVST_0.2-1             pkgmaker_0.22          withr_2.1.0           
[133] qlcMatrix_0.9.5        mnormt_1.5-5           diptest_0.75-7         grid_3.4.2            
[137] rpart_4.1-11           timeDate_3042.101      tidyr_0.7.2            class_7.3-14          
[141] segmented_0.5-3.0      Rtsne_0.13             git2r_0.19.0           numDeriv_2016.8-1     
[145] scatterplot3d_0.3-40   lubridate_1.7.1        base64enc_0.1-3    

Could anybody help me?

Thank you!
M

[serghiou]

Hi there,

I had the same issue. As per guidance given by this repo, first go to the Terminal and type:

brew install homebrew/science/hdf5 --enable-cxx

Then, load R and try to install again:

install.packages("h5")

This did it for me :)

[marzamKI]

Hey,
Thank you for your reply.
I've tried. Also tried re-installing R now, but it doesn't work.

On the terminal I get this warnings:

c5-a2RX0PGFVH8:build margherita$ brew install homebrew/science/hdf5 --enable-cxx
Warning: Use hdf5 instead of deprecated homebrew/science/hdf5
Warning: hdf5: this formula has no --enable-cxx option so it will be ignored!
==> Downloading https://homebrew.bintray.com/bottles/hdf5-1.10.1_2.high_sierra.bottle.tar.gz
Already downloaded: /Users/margheritazamboni/Library/Caches/Homebrew/hdf5-1.10.1_2.high_sierra.bottle.tar.gz
==> Pouring hdf5-1.10.1_2.high_sierra.bottle.tar.gz
🍺  /usr/local/Cellar/hdf5/1.10.1_2: 265 files, 14.6MB

(Then I've tried to download hdf5 instead of homebrew/science/hdf5, but nothing has changed).

Cheers,
M

[heroxbd]

"hdf5: this formula has no --enable-cxx option so it will be ignored!" means that you have never compiled hdf5 with cxx support.