Problem installing nichenetr #45
Comments
|
Hi @Dahlia90 Are you sure you ran this command to install nichenetr? This should work for R 4.0.2 (I tested it on Windows 10 and Ubuntu 20.04). If not, please give your R ``sessionInfo()` details. |
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Hey Robin,
Yes, I installed it using this command.
session_info()
─ Session info
──────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os macOS Catalina 10.15.5
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Asia/Tokyo
date 2020-08-04
─ Packages
──────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2)
ape 5.4 2020-06-03 [1] CRAN (R 4.0.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.8 2020-06-17 [1] CRAN (R 4.0.0)
Biobase 2.49.0 2020-05-14 [1] Bioconductor
BiocGenerics 0.35.4 2020-06-04 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
broom 0.7.0 2020-07-09 [1] CRAN (R 4.0.2)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2)
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.2)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
cowplot 1.0.0 2019-07-11 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
data.table 1.13.0 2020-07-24 [1] CRAN (R 4.0.2)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.0)
DelayedArray 0.15.7 2020-07-14 [1] Bioconductor
deldir 0.1-28 2020-07-15 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools * 2.3.1 2020-07-21 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
dplyr * 1.0.1 2020-07-31 [1] CRAN (R 4.0.2)
dyndimred 1.0.3 2020-03-08 [1] CRAN (R 4.0.0)
dynutils 1.0.5 2020-02-21 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.0)
fitdistrplus 1.1-1 2020-05-19 [1] CRAN (R 4.0.0)
forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.0)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
future 1.18.0 2020-07-09 [1] CRAN (R 4.0.2)
future.apply 1.6.0 2020-07-01 [1] CRAN (R 4.0.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
GenomeInfoDb 1.25.8 2020-07-03 [1] Bioconductor
GenomeInfoDbData 1.2.3 2020-06-19 [1] Bioconductor
GenomicRanges 1.41.5 2020-06-09 [1] Bioconductor
ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.0)
ggrepel 0.8.2 2020-03-08 [1] CRAN (R 4.0.0)
ggridges 0.5.2 2020-01-12 [1] CRAN (R 4.0.0)
globals 0.12.5 2019-12-07 [1] CRAN (R 4.0.0)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
goftest 1.2-2 2019-12-02 [1] CRAN (R 4.0.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
haven 2.3.1 2020-06-01 [1] CRAN (R 4.0.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.0)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.0)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
ica 1.0-2 2018-05-24 [1] CRAN (R 4.0.0)
igraph * 1.2.5 2020-03-19 [1] CRAN (R 4.0.0)
IRanges 2.23.10 2020-06-13 [1] Bioconductor
irlba 2.3.3 2019-02-05 [1] CRAN (R 4.0.0)
jsonlite 1.7.0 2020-06-25 [1] CRAN (R 4.0.0)
KernSmooth 2.23-17 2020-04-26 [1] CRAN (R 4.0.2)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.0)
leiden * 0.3.3 2020-02-04 [1] CRAN (R 4.0.0)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
limma * 3.45.9 2020-07-14 [1] Bioconductor
listenv 0.8.0 2019-12-05 [1] CRAN (R 4.0.0)
lmds 0.1.0 2019-09-27 [1] CRAN (R 4.0.0)
lmtest 0.9-37 2019-04-30 [1] CRAN (R 4.0.0)
lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
MASS 7.3-51.6 2020-04-26 [1] CRAN (R 4.0.2)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.2)
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
mgcv 1.8-31 2019-11-09 [1] CRAN (R 4.0.2)
mime 0.9 2020-02-04 [1] CRAN (R 4.0.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.2)
modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
nlme 3.1-148 2020-05-24 [1] CRAN (R 4.0.2)
patchwork 1.0.1 2020-06-22 [1] CRAN (R 4.0.0)
pbapply 1.4-2 2019-08-31 [1] CRAN (R 4.0.0)
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
plotly 4.9.2.1 2020-04-04 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0)
polyclip 1.10-0 2019-03-14 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
princurve * 2.1.4 2019-05-29 [1] CRAN (R 4.0.0)
processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.2)
promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.0)
proxyC 0.1.5 2019-07-21 [1] CRAN (R 4.0.0)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
RANN 2.6.1 2019-01-08 [1] CRAN (R 4.0.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
RcppAnnoy 0.0.16 2020-03-08 [1] CRAN (R 4.0.0)
RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.0)
RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0)
readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.0)
readxl 1.3.1 2019-03-13 [1] CRAN (R 4.0.0)
remotes * 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.0)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.0)
reticulate * 1.16 2020-05-27 [1] CRAN (R 4.0.0)
rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.0.0)
rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
rsvd 1.0.3 2020-02-17 [1] CRAN (R 4.0.0)
Rtsne 0.15 2018-11-10 [1] CRAN (R 4.0.0)
rvest 0.3.6 2020-07-25 [1] CRAN (R 4.0.2)
S4Vectors 0.27.12 2020-06-09 [1] Bioconductor
scales * 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
sctransform 0.2.1 2019-12-17 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
Seurat * 3.2.0 2020-07-16 [1] CRAN (R 4.0.2)
shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.0)
SingleCellExperiment 1.11.6 2020-06-26 [1] Bioconductor
slingshot * 1.7.3 2020-07-15 [1] Bioconductor
spatstat 1.64-1 2020-05-12 [1] CRAN (R 4.0.2)
spatstat.data 1.4-3 2020-01-26 [1] CRAN (R 4.0.2)
spatstat.utils 1.17-0 2020-02-07 [1] CRAN (R 4.0.2)
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
SummarizedExperiment 1.19.6 2020-07-09 [1] Bioconductor
survival 3.2-3 2020-06-13 [1] CRAN (R 4.0.2)
tensor 1.5 2012-05-05 [1] CRAN (R 4.0.2)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
tibble * 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
tidyr * 1.1.1 2020-07-31 [1] CRAN (R 4.0.2)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.0)
tinytex 0.25 2020-07-24 [1] CRAN (R 4.0.2)
usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.0)
vctrs 0.3.2 2020-07-15 [1] CRAN (R 4.0.2)
viridis * 0.5.1 2018-03-29 [1] CRAN (R 4.0.0)
viridisLite * 0.3.0 2018-02-01 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
xfun 0.16 2020-07-24 [1] CRAN (R 4.0.2)
xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
XVector 0.29.3 2020-06-25 [1] Bioconductor
zlibbioc 1.35.0 2020-05-14 [1] Bioconductor
zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.0)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
…On Tue, Aug 4, 2020 at 3:51 PM Robin Browaeys ***@***.***> wrote:
Hi @Dahlia90 <https://github.com/Dahlia90>
Are you sure you ran this command to install nichenetr?
devtools::install_github("saeyslab/nichenetr")
This should work for R 4.0.2 (I tested it on Windows 10 and Ubuntu 20.04).
If not, please give your R ``sessionInfo()` details.
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Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
Hi @Dahlia90 Can you tell me whether you are able to install other packages from github via devtools::install_github to check whether it is a devtools/github or nichenetr problem? Recently, another Mac user had problems installing nichenetr as well (#42) |
|
I just tried to download two packages using devtools::install_github
(viridis & rgl),but only the former got installed.
…On Tue, Aug 4, 2020 at 4:20 PM Robin Browaeys ***@***.***> wrote:
Hi @Dahlia90 <https://github.com/Dahlia90>
Can you tell me whether you are able to install other packages from github
via devtools::install_github to check whether it is a devtools/github or
nichenetr problem?
Recently, another Mac user had problems installing nichenetr as well (#42
<#42>)
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Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
Hi @Dahlia90 Could you maybe try to install nichenetr from an older R version (3.6.X or 4.0.0? - I know from a colleague that it gets installed when having R 4.0.0) to check whether this is an R version problem? |
|
Yeah, I thought about doing that until my colleague told me he downloaded
it and is successfully using it on R version 4.0.2 on mac.
…On Wed, Aug 5, 2020 at 3:51 PM Robin Browaeys ***@***.***> wrote:
Hi @Dahlia90 <https://github.com/Dahlia90>
Could you maybe try to install nichenetr from an older R version (3.6.X or
4.0.0? - I know from a colleague that it gets installed when having R
4.0.0) to check whether this is an R version problem?
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--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
OK, then it seems it has more likely something to do with your pc settings. I would suggest comparing them to your colleague's and trying to find the issue by doing that. I am sorry that I cannot give any further recommendations to try out to. If you would be able to solve the issue, it would be nice that you let us know here how you did it, because probably some other people might get stuck with the same problem. |
|
I checked with him and I did the following:
1- Updated Rstudio
2- Tried remotes::install_github to overcome lazyloading
3- Attempted to download it through terminal
devtools::install.github("sayeyslab/nichenetr")
4- Installed C++ compiler on terminal, Rcpp, clang & made an environmental
file
5- Checked the environmental variables on mac
But it's still not working.
…On Wed, Aug 5, 2020 at 4:06 PM Robin Browaeys ***@***.***> wrote:
OK, then it seems it has more likely something to do with your pc
settings. I would suggest comparing them to your colleague's and trying to
find the issue by doing that. I am sorry that I cannot give any further
recommendations to try out to. If you would be able to solve the issue, it
would be nice that you let us know here how you did it, because probably
some other people might get stuck with the same problem.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#45 (comment)>,
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--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
And can you give the exact error message? |
|
(1) > install.packages(“saeyslab/nichenetr”)
Warning in install.packages :
package ‘saeyslab/nichenetr’ is not available (for R version 4.0.2)
(2) Every time I install through devtools on r, I get the same error (even
after installing "limma"):
devtools::install_github(“saeyslab/nichenetr”)
Downloading GitHub repo saeyslab/nichenetr@HEAD
Skipping 1 packages not available: limma
✓ checking for file
‘/private/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T/Rtmp4U4Yop/remotes7b3956335f00/saeyslab-nichenetr-8b2fffc/DESCRIPTION’
(359ms)
─ preparing ‘nichenetr’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘nichenetr_1.0.0.tar.gz’* installing *source* package
‘nichenetr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 32208 Killed: 9 R_TESTS=
‘/Library/Frameworks/R.framework/Resources/bin/R’ --no-save --no-restore
--no-echo 2>&1 <
‘/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T//RtmpwecKir/file7dc66f5800e’
ERROR: lazy loading failed for package ‘nichenetr’
* removing
‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/nichenetr’
Error: Failed to install ‘nichenetr’ from GitHub:
(converted from warning) installation of package
‘/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T//Rtmp4U4Yop/file7b3946a22536/nichenetr_1.0.0.tar.gz’
had non-zero exit status
(3) When I try to download on terminal:
(base) Dahlias-MacBook-Air:~ deldeeb$
devtools::install.github(“sayeyslab/nitchnetr”)
-bash: syntax error near unexpected token `“sayeyslab/nitchnetr”'
…On Wed, Aug 5, 2020 at 5:28 PM Robin Browaeys ***@***.***> wrote:
And can you give the exact error message?
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--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
Hi @Dahlia90 (1): nichenetr is not on CRAN, so this will never work |
|
(2) Yes for limma & yes for arranging the ~/.R/Makevars as the issue you
recommended.
(3) I'm sorry, I actually fixed the spelling when I ran the command & still
got the error.
So now that leaves me to cloning the nichenetr directory.
…On Wed, Aug 5, 2020 at 5:56 PM Robin Browaeys ***@***.***> wrote:
Hi @Dahlia90 <https://github.com/Dahlia90>
(1): nichenetr is not on CRAN, so this will never work
(2): did you install limma via BiocManager::install("limma")? and can you
afterwords load the package library(limma)? If both answers are yes,
maybe it could be useful to check out this issue hunzikp/velox#30
<hunzikp/velox#30>. If those tips would still
not work, you could clone the nichenetr directory so you get the repo
locally and then install it locally from within R studio.
(3): running a devtools command in bash will not work, so you would need
to run R first, and then fix the typos in “sayeyslab/nitchnetr” to
"saeyslab/nichenetr”
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--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
Hey Robin,
I cloned the directory & when I tried:
*> devtools::install_github("saeyslab/nichenetr")*Downloading GitHub repo
saeyslab/nichenetr@HEAD
Skipping 1 packages not available: limma
✓ checking for file
‘/private/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T/RtmpYSFolX/remotes9eed36454700/saeyslab-nichenetr-8b2fffc/DESCRIPTION’
...
─ preparing ‘nichenetr’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘nichenetr_1.0.0.tar.gz’
* installing *source* package ‘nichenetr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 41083 Killed: 9 R_TESTS=
'/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore
--no-echo 2>&1 <
'/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T//RtmpCHZzIz/filea0732cc06b88'
ERROR: lazy loading failed for package ‘nichenetr’
* removing
‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/nichenetr’
Error: Failed to install 'nichenetr' from GitHub:
(converted from warning) installation of package
‘/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T//RtmpYSFolX/file9eed7e386cd5/nichenetr_1.0.0.tar.gz’
had non-zero exit status
Then I tried:
*> library(limma)> devtools::install_github("saeyslab/nichenetr", args =
"--no-test-load")*
Downloading GitHub repo saeyslab/nichenetr@HEAD
Skipping 1 packages not available: limma
✓ checking for file
‘/private/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T/RtmpYSFolX/remotes9eed469a7002/saeyslab-nichenetr-8b2fffc/DESCRIPTION’
...
─ preparing ‘nichenetr’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘nichenetr_1.0.0.tar.gz’
* installing *source* package ‘nichenetr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 41302 Killed: 9 R_TESTS=
'/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore
--no-echo 2>&1 <
'/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T//RtmpuNkej5/filea14e50d380c2'
ERROR: lazy loading failed for package ‘nichenetr’
* removing
‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/nichenetr’
Error: Failed to install 'nichenetr' from GitHub:
(converted from warning) installation of package
‘/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T//RtmpYSFolX/file9eed452fb784/nichenetr_1.0.0.tar.gz’
had non-zero exit status
Warning message:
1 components of `...` were not used.
We detected these problematic arguments:
* `args`
Did you misspecify an argument?
On Wed, Aug 5, 2020 at 8:55 PM DAHLIA ELDEEB <
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp> wrote:
… (2) Yes for limma & yes for arranging the ~/.R/Makevars as the issue you
recommended.
(3) I'm sorry, I actually fixed the spelling when I ran the command &
still got the error.
So now that leaves me to cloning the nichenetr directory.
On Wed, Aug 5, 2020 at 5:56 PM Robin Browaeys ***@***.***>
wrote:
> Hi @Dahlia90 <https://github.com/Dahlia90>
>
> (1): nichenetr is not on CRAN, so this will never work
> (2): did you install limma via BiocManager::install("limma")? and can
> you afterwords load the package library(limma)? If both answers are yes,
> maybe it could be useful to check out this issue hunzikp/velox#30
> <hunzikp/velox#30>. If those tips would still
> not work, you could clone the nichenetr directory so you get the repo
> locally and then install it locally from within R studio.
> (3): running a devtools command in bash will not work, so you would need
> to run R first, and then fix the typos in “sayeyslab/nitchnetr” to
> "saeyslab/nichenetr”
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#45 (comment)>,
> or unsubscribe
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> .
>
--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
***@***.***
080 9649 1437
--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
Hi @Dahlia90 |
|
Thanks a lot for following up.
I just did as you recommended:
==> R CMD INSTALL --no-multiarch --with-keep.source nichenetr
* installing to library
‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘nichenetr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 1900 Killed: 9 R_TESTS=
'/Library/Frameworks/R.framework/Resources/bin/R' --no-save
--no-restore --no-echo 2>&1 <
'/var/folders/3v/vq2xx_vd2rg882nmxfcrxpdm0000gn/T//RtmpzXBwg3/file76253b140e8'ERROR:
lazy loading failed for package ‘nichenetr’* removing
‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/nichenetr’
Exited with status 1.
…On Thu, Aug 6, 2020 at 3:55 PM Robin Browaeys ***@***.***> wrote:
Hi @Dahlia90 <https://github.com/Dahlia90>
Thank you for pointing this out, but this is just a warning and not an
error, and not a reason why this failed.
But here you again installed from github. I would try to install it
locally as follows: clone the directory from github --> go to the nichenetr
directory --> open the nichenetr R project in Rstudio --> go to 'Build' in
Rstudio --> 'Install'
and see whether this gives the same error message.
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--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
Hi @Dahlia90 Sorry it did not work. Unfortunately for you and me, this error message is not really helpful. I have no idea what is going on. By looking around the web for possible solutions, I did not come across any directly but I can give some suggestions to try out: *The error 1900 Killed: 9 points to a non-nichenetr problem, but probably to an error in the combination Mac-Rstudio-nichenetr (it seems that issues with Rstudio, Rstudio Cloud/Server, Docker, Conda, ... could be occuring).
If all these steps still failed:
|
|
Hey Robin,
Thanks a lot for your patience. I’ll try those tips today. I understand if
you’ll have to close this issue. Thanks a lot for your help.
On Fri, Aug 7, 2020 at 0:32 Robin Browaeys ***@***.***> wrote:
Hi @Dahlia90 <https://github.com/Dahlia90>
Sorry it did not work. Unfortunately for you and me, this error message is
not really helpful. I have no idea what is going on. By looking around the
web for possible solutions, I did not come across any directly but I can
give some suggestions to try out:
*The error 1900 Killed: 9 points to a non-nichenetr problem, but probably
to an error in the combination Mac-Rstudio-nichenetr (it seems that issues
with Rstudio, Rstudio Cloud/Server, Docker, Conda, ... could be occuring).
If you were installing nichenetr from RStudio, I would
1. first try to install nichenetr from a clean R session on the
command line (so: open terminal --> launch R 4.0.2 -->
devtools::install_github("saeyslab/nichenetr").
2. If that fails, and you have a form of Conda (e.g. Miniconda)
installed on your computer, maybe remove it and then try to install
nichenetr again
3. if that still fails: try reinstalling R and RStudio (downloading R
from CRAN, and RStudio from rstudio.com), then install nichenetr (try
Rstudio and R via terminal).
4. if that still fails: check the DESCRIPTION page of nichenetr and
install each of the dependencies separately and then try to install
nichenetr again.
If all these steps still failed:
you can check following sites for more information and see whether they
might be useful for you:
- https://github.com/jacobxk/setup_macOS_for_R
-
https://stackoverflow.com/questions/19533220/cannot-install-r-package-from-source-in-mac-osx-maverick
-
https://community.rstudio.com/t/killed-error-during-installation-for-many-packages/24239/8
-
https://stackoverflow.com/questions/58473798/macos-rstudio-accessing-wrong-clang-after-upgrade-to-catalina
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--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
|
Hey Robin,
I have installed the dependencies one by one and I could finally install
nichenetr.
Thanks a lot for your help.
On Fri, Aug 7, 2020 at 8:51 AM DAHLIA ELDEEB <
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp> wrote:
… Hey Robin,
Thanks a lot for your patience. I’ll try those tips today. I understand if
you’ll have to close this issue. Thanks a lot for your help.
On Fri, Aug 7, 2020 at 0:32 Robin Browaeys ***@***.***>
wrote:
> Hi @Dahlia90 <https://github.com/Dahlia90>
>
> Sorry it did not work. Unfortunately for you and me, this error message
> is not really helpful. I have no idea what is going on. By looking around
> the web for possible solutions, I did not come across any directly but I
> can give some suggestions to try out:
>
> *The error 1900 Killed: 9 points to a non-nichenetr problem, but probably
> to an error in the combination Mac-Rstudio-nichenetr (it seems that issues
> with Rstudio, Rstudio Cloud/Server, Docker, Conda, ... could be occuring).
> If you were installing nichenetr from RStudio, I would
>
> 1. first try to install nichenetr from a clean R session on the
> command line (so: open terminal --> launch R 4.0.2 -->
> devtools::install_github("saeyslab/nichenetr").
> 2. If that fails, and you have a form of Conda (e.g. Miniconda)
> installed on your computer, maybe remove it and then try to install
> nichenetr again
> 3. if that still fails: try reinstalling R and RStudio (downloading R
> from CRAN, and RStudio from rstudio.com), then install nichenetr (try
> Rstudio and R via terminal).
> 4. if that still fails: check the DESCRIPTION page of nichenetr and
> install each of the dependencies separately and then try to install
> nichenetr again.
>
> If all these steps still failed:
> you can check following sites for more information and see whether they
> might be useful for you:
>
> - https://github.com/jacobxk/setup_macOS_for_R
> -
> https://stackoverflow.com/questions/19533220/cannot-install-r-package-from-source-in-mac-osx-maverick
> -
> https://community.rstudio.com/t/killed-error-during-installation-for-many-packages/24239/8
> -
> https://stackoverflow.com/questions/58473798/macos-rstudio-accessing-wrong-clang-after-upgrade-to-catalina
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#45 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AONSFJ4NRT7LDIIQBZ4M4MLR7LEKLANCNFSM4PT4S5PA>
> .
>
--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
***@***.***
080 9649 1437
--
Regards,
Dahlia Eldeeb
PhD student at the Laboratory of Clinical Biotechnology
Graduate school of medicine, The University of Tokyo
dahlia-eldeeb@g.ecc.u-tokyo.ac.jp
080 9649 1437
|
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Hello,
I've tried to install nichenetr on r version 4.0.2, but it's not available on this version.
Is there an older version to download and install on r version 4.0.2?
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