jokergoo
commented
3 years ago What is the error message?
Maybe you should also update ComplexHeatmap from GitHub.
Closed klai001 closed 3 years ago
jokergoo
commented
3 years ago What is the error message?
Maybe you should also update ComplexHeatmap from GitHub.
klai001
commented
3 years ago `Warning message: package ‘InteractiveComplexHeatmap’ is not available for this version of R
A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages `
that's the error msg ^
`> sessionInfo() R version 4.0.4 (2021-02-15) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 15063)
Matrix products: default
locale:
[1] LC_COLLATE=English_Singapore.1252 LC_CTYPE=English_Singapore.1252
[3] LC_MONETARY=English_Singapore.1252 LC_NUMERIC=C
[5] LC_TIME=English_Singapore.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] BiocManager_1.30.10 compiler_4.0.4 tools_4.0.4 `
klai001
commented
3 years ago I updated ComplexHeatmap from github without any issues; however i still get the following error when i try to install the Github's version of Interactive Complex Heatmap
`> install_github("jokergoo/InteractiveComplexHeatmap") Downloading GitHub repo jokergoo/InteractiveComplexHeatmap@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?
1: All
2: CRAN packages only
3: None
4: glue (1.4.1 -> 1.4.2) [CRAN]
5: fansi (0.4.1 -> 0.4.2) [CRAN]
Enter one or more numbers, or an empty line to skip updates:1 processx (NA -> 3.5.0) [CRAN] glue (1.4.1 -> 1.4.2) [CRAN] fansi (0.4.1 -> 0.4.2) [CRAN] clisymbols (NA -> 1.2.0) [CRAN] kableExtra (NA -> 1.3.4) [CRAN] Installing 5 packages: processx, glue, fansi, clisymbols, kableExtra Installing packages into ‘C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages’ (as ‘lib’ is unspecified)
There is a binary version available but the source version is later: binary source needs_compilation processx 3.4.5 3.5.0 TRUE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/glue_1.4.2.zip' Content type 'application/zip' length 154862 bytes (151 KB) downloaded 151 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/fansi_0.4.2.zip' Content type 'application/zip' length 223909 bytes (218 KB) downloaded 218 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/clisymbols_1.2.0.zip' Content type 'application/zip' length 21106 bytes (20 KB) downloaded 20 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/kableExtra_1.3.4.zip' Content type 'application/zip' length 1853720 bytes (1.8 MB) downloaded 1.8 MB
package ‘glue’ successfully unpacked and MD5 sums checked Error: Failed to install 'InteractiveComplexHeatmap' from GitHub: (converted from warning) cannot remove prior installation of package ‘glue’
remove.packages("glue") Removing package from ‘C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages’ (as ‘lib’ is unspecified) Error in remove.packages : there is no package called ‘glue’ install_github("jokergoo/InteractiveComplexHeatmap") Downloading GitHub repo jokergoo/InteractiveComplexHeatmap@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?
1: All
2: CRAN packages only
3: None
4: fansi (0.4.1 -> 0.4.2) [CRAN]
Enter one or more numbers, or an empty line to skip updates:1 processx (NA -> 3.5.0) [CRAN] glue (NA -> 1.4.2) [CRAN] fansi (0.4.1 -> 0.4.2) [CRAN] clisymbols (NA -> 1.2.0) [CRAN] kableExtra (NA -> 1.3.4) [CRAN] Installing 5 packages: processx, glue, fansi, clisymbols, kableExtra Installing packages into ‘C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages’ (as ‘lib’ is unspecified)
There is a binary version available but the source version is later: binary source needs_compilation processx 3.4.5 3.5.0 TRUE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/glue_1.4.2.zip' Content type 'application/zip' length 154862 bytes (151 KB) downloaded 151 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/fansi_0.4.2.zip' Content type 'application/zip' length 223909 bytes (218 KB) downloaded 218 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/clisymbols_1.2.0.zip' Content type 'application/zip' length 21106 bytes (20 KB) downloaded 20 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/kableExtra_1.3.4.zip' Content type 'application/zip' length 1853720 bytes (1.8 MB) downloaded 1.8 MB
package ‘glue’ successfully unpacked and MD5 sums checked Error: Failed to install 'InteractiveComplexHeatmap' from GitHub: (converted from warning) cannot remove prior installation of package ‘glue’
install_github("jokergoo/InteractiveComplexHeatmap") Downloading GitHub repo jokergoo/InteractiveComplexHeatmap@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?
1: All
2: CRAN packages only
3: None
4: fansi (0.4.1 -> 0.4.2) [CRAN]
Enter one or more numbers, or an empty line to skip updates:3 Installing 4 packages: processx, glue, clisymbols, kableExtra Installing packages into ‘C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages’ (as ‘lib’ is unspecified)
There is a binary version available but the source version is later: binary source needs_compilation processx 3.4.5 3.5.0 TRUE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/glue_1.4.2.zip' Content type 'application/zip' length 154862 bytes (151 KB) downloaded 151 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/clisymbols_1.2.0.zip' Content type 'application/zip' length 21106 bytes (20 KB) downloaded 20 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/kableExtra_1.3.4.zip' Content type 'application/zip' length 1853720 bytes (1.8 MB) downloaded 1.8 MB
package ‘glue’ successfully unpacked and MD5 sums checked Error: Failed to install 'InteractiveComplexHeatmap' from GitHub: (converted from warning) cannot remove prior installation of package ‘glue’`
the following error msg appears when i try to install BioConductor version of Interactive Complex heatmap
> BiocManager::install("InteractiveComplexHeatmap")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.4 (2021-02-15)
Installing package(s) 'InteractiveComplexHeatmap'
Old packages: 'fansi', 'pkgload', 'psych', 'RSQLite', 'testthat', 'tweenr'
Update all/some/none? [a/s/n]:
a
also installing the dependency ‘processx’
There are binary versions available but the source versions are later:
binary source needs_compilation
processx 3.4.5 3.5.0 TRUE
psych 2.0.12 2.1.3 FALSE
RSQLite 2.2.4 2.2.5 TRUE
tweenr 1.0.1 1.0.2 TRUE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/fansi_0.4.2.zip'
Content type 'application/zip' length 223909 bytes (218 KB)
downloaded 218 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/pkgload_1.2.0.zip'
Content type 'application/zip' length 152082 bytes (148 KB)
downloaded 148 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/testthat_3.0.2.zip'
Content type 'application/zip' length 2496220 bytes (2.4 MB)
downloaded 2.4 MB
package ‘fansi’ successfully unpacked and MD5 sums checked
package ‘pkgload’ successfully unpacked and MD5 sums checked
package ‘testthat’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Lim Peck Hui\AppData\Local\Temp\Rtmp6FcMAX\downloaded_packages
installing the source packages ‘processx’, ‘psych’, ‘RSQLite’, ‘tweenr’
trying URL 'https://cran.rstudio.com/src/contrib/processx_3.5.0.tar.gz'
Content type 'application/x-gzip' length 138856 bytes (135 KB)
downloaded 135 KB
trying URL 'https://cran.rstudio.com/src/contrib/psych_2.1.3.tar.gz'
Content type 'application/x-gzip' length 1978624 bytes (1.9 MB)
downloaded 1.9 MB
trying URL 'https://cran.rstudio.com/src/contrib/RSQLite_2.2.5.tar.gz'
Content type 'application/x-gzip' length 2471348 bytes (2.4 MB)
downloaded 2.4 MB
trying URL 'https://cran.rstudio.com/src/contrib/tweenr_1.0.2.tar.gz'
Content type 'application/x-gzip' length 568677 bytes (555 KB)
downloaded 555 KB
* installing *source* package 'processx' ...
** package 'processx' successfully unpacked and MD5 sums checked
** using staged installation
** libs
*** arch - i386
"c:/rtools40/mingw32/bin/"gcc -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -Wall tools/px.c -o tools/px.exe
sh: c:/rtools40/mingw32/bin/gcc: No such file or directory
make: *** [Makevars.win:18: tools/px.exe] Error 127
ERROR: compilation failed for package 'processx'
* removing 'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/processx'
* installing *source* package 'psych' ...
** package 'psych' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'psych'
finding HTML links ... done
00.psych-package html
AUC html
Garcia html
Gleser html
Gorsuch html
Harman html
ICC html
ICLUST html
ICLUST.cluster html
ICLUST.graph html
ICLUST.rgraph html
ICLUST.sort html
KMO html
Pinv html
Promax html
SD html
Schmid.Leiman html
Tucker html
VSS html
VSS.parallel html
VSS.plot html
VSS.scree html
Yule html
alpha html
anova.psych html
bassAckward html
best.scales html
bfi html
bi.bars html
bifactor html
biplot.psych html
block.random html
bock.table html
cattell html
circ.tests html
cluster.cor html
cluster.fit html
cluster.loadings html
cluster.plot html
cluster2keys html
cohen.d html
comorbidity html
cor.ci html
cor.plot html
cor.smooth html
cor.wt html
cor2dist html
corFiml html
corr.test html
correct.cor html
cortest.bartlett html
cortest.mat html
cosinor html
count.pairwise html
cta html
densityBy html
deprecated html
describe html
describe.by html
diagram html
draw.tetra html
dummy.code html
dwyer html
eigen.loadings html
ellipses html
error.bars html
error.bars.by html
error.circles html
error.crosses html
error.dots html
esem html
fa html
fa.diagram html
fa.extension html
fa.lookup html
fa.parallel html
fa.random html
fa.sort html
faCor html
faMulti html
factor.congruence html
factor.fit html
factor.model html
factor.residuals html
factor.rotate html
factor.scores html
factor.stats html
factor2cluster html
fisherz html
fparse html
geometric.mean html
glb.algebraic html
guttman html
harmonic.mean html
headtail html
iclust.diagram html
interp.median html
irt.fa html
irt.item.diff.rasch html
irt.person.rasch html
irt.responses html
kaiser html
kappa html
logistic html
lowerUpper html
make.keys html
manhattan html
mat.sort html
matrix.addition html
mediate html
misc html
mixed.cor html
mssd html
multi.hist html
multilevel.reliability html
omega html
omega.graph html
outlier html
p.rep html
paired.r html
pairs.panels html
parcels html
partial.r html
phi html
phi.demo html
phi2poly html
plot.psych html
polar html
polychor.matrix html
predict.psych html
principal html
print.psych html
r.test html
range.correction html
rescale html
residuals.psych html
reverse.code html
sat.act html
scaling.fits html
scatter.hist html
schmid html
score.alpha html
score.irt html
score.items html
score.multiple.choice html
scoreWtd html
scrub html
set.cor html
sim html
sim.VSS html
sim.anova html
sim.congeneric html
sim.hierarchical html
sim.irt html
sim.item html
sim.multilevel html
sim.omega html
sim.structural html
simulation.circ html
skew html
smc html
spengler html
spider html
statsBy html
structure.diagram html
structure.list html
super.matrix html
table2matrix html
tal_or html
test.irt html
test.psych html
testRetest html
tetrachor html
thurstone html
tr html
unidim html
winsor html
withinBetween html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (psych)
* installing *source* package 'RSQLite' ...
** package 'RSQLite' successfully unpacked and MD5 sums checked
** using staged installation
** libs
*** arch - i386
"c:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.4/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/BH/include' -I'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/plogr/include' -I'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/Rcpp/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DbColumn.cpp -o DbColumn.o
sh: c:/rtools40/mingw32/bin/g++: No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.4/etc/i386/Makeconf:229: DbColumn.o] Error 127
ERROR: compilation failed for package 'RSQLite'
* removing 'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/RSQLite'
* restoring previous 'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/RSQLite'
* installing *source* package 'tweenr' ...
** package 'tweenr' successfully unpacked and MD5 sums checked
** using staged installation
** libs
*** arch - i386
"c:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.4/include" -DNDEBUG -I'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/Rcpp/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
sh: c:/rtools40/mingw32/bin/g++: No such file or directory
make: *** [C:/PROGRA~1/R/R-40~1.4/etc/i386/Makeconf:229: RcppExports.o] Error 127
ERROR: compilation failed for package 'tweenr'
* removing 'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/tweenr'
* restoring previous 'C:/UsersLim Peck Hui/AppData/Local/Temp/RtmpKoIUzm/downloaded_packages/tweenr'
The downloaded source packages are in
‘C:\Users\Lim Peck Hui\AppData\Local\Temp\Rtmp6FcMAX\downloaded_packages’
Warning messages:
1: package ‘InteractiveComplexHeatmap’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘processx’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘RSQLite’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘tweenr’ had non-zero exit statusHi Zuguang i manged to resolve the issues turns out my Rstudio couldnt recognise Rtools downloaded
Hi Zuguang
I am extremely keen to try out InteractiveComplex Heatmap However; i tried installing the package but there is in an error which says the R version is not suitable my console is currently 4.04 (already the latest) on Windows and i noticed that the biocondutor page for interactive complexheatmap says 4.1 is required.
I tried both installing on github and bioC but both doesnt allow me to install it. Could you direct me to where i can install for R 4.04 Windows? thanks