Installation failed #66
Description
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