Error: package or namespace load failed for ‘celda’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘GenomeInfoDbData’
Closed this issue · 1 comments
Hi,
when I try to install the package by using conda, I get the error:
Error: package or namespace load failed for ‘celda’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Actually I have downloaded the GenomeInfoDbData package using conda, I dont known how to install celda package,please help me.
Installing the package on a separate linux cluster worked for me with the same R version (R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)).
here is my conda list:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
argcomplete 1.12.3 pyhd3eb1b0_0
atk-1.0 2.36.0 ha1a6a79_0
binutils_impl_linux-64 2.38 h2a08ee3_1
bioconductor-basilisk 1.2.1 r40hdfd78af_0 bioconda
bioconductor-basilisk.utils 1.2.2 r40hdfd78af_0 bioconda
bioconductor-beachmat 2.6.4 r40h399db7b_1 bioconda
bioconductor-biobase 2.50.0 r40hd029910_1 bioconda
bioconductor-biocgenerics 0.36.0 r40hdfd78af_1 bioconda
bioconductor-biocneighbors 1.8.2 r40h399db7b_0 bioconda
bioconductor-biocparallel 1.24.1 r40h399db7b_0 bioconda
bioconductor-biocsingular 1.6.0 r40h399db7b_1 bioconda
bioconductor-bluster 1.0.0 r40hf484d3e_0 paul.martin-2
bioconductor-celda 1.6.1 r40h399db7b_1 bioconda
bioconductor-complexheatmap 2.6.2 r40hdfd78af_1 bioconda
bioconductor-data-packages 20230718 hdfd78af_1 bioconda
bioconductor-delayedarray 0.16.3 r40hd029910_0 bioconda
bioconductor-delayedmatrixstats 1.12.3 r40hdfd78af_0 bioconda
bioconductor-densvis 1.00.6 r40h399db7b_0 bioconda
bioconductor-edger 3.32.1 r40h399db7b_0 bioconda
bioconductor-genomeinfodb 1.26.4 r40hdfd78af_0 bioconda
bioconductor-genomeinfodbdata 1.2.4 r40hdfd78af_2 bioconda
bioconductor-genomicranges 1.42.0 r40hd029910_1 bioconda
bioconductor-hdf5array 1.18.1 r40hd029910_0 bioconda
bioconductor-iranges 2.24.1 r40hd029910_0 bioconda
bioconductor-limma 3.46.0 r40hd029910_1 bioconda
bioconductor-mast 1.16.0 r40hdfd78af_1 bioconda
bioconductor-matrixgenerics 1.2.1 r40hdfd78af_0 bioconda
bioconductor-rhdf5 2.34.0 r40h399db7b_1 bioconda
bioconductor-rhdf5filters 1.2.0 r40h399db7b_1 bioconda
bioconductor-rhdf5lib 1.12.1 r40hd029910_0 bioconda
bioconductor-s4vectors 0.28.1 r40hd029910_0 bioconda
bioconductor-scater 1.18.6 r40hdfd78af_0 bioconda
bioconductor-scran 1.18.5 r40h399db7b_0 bioconda
bioconductor-scuttle 1.0.4 r40h399db7b_0 bioconda
bioconductor-singlecellexperiment 1.12.0 r40hdfd78af_1 bioconda
bioconductor-sparsematrixstats 1.2.1 r40h399db7b_0 bioconda
bioconductor-summarizedexperiment 1.20.0 r40hdfd78af_1 bioconda
bioconductor-xvector 0.30.0 r40hd029910_1 bioconda
bioconductor-zlibbioc 1.36.0 r40hd029910_1 bioconda
boost-cpp 1.81.0 he95ae9e_0 conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7b6447c_0
c-ares 1.23.0 hd590300_0 conda-forge
ca-certificates 2023.11.17 hbcca054_0 conda-forge
cairo 1.16.0 hb05425b_5
curl 7.86.0 h2283fc2_1 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fftw 3.3.10 nompi_hc118613_108 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc_impl_linux-64 12.1.0 hea43390_17 conda-forge
gdk-pixbuf 2.42.10 h5eee18b_0
gettext 0.21.1 h27087fc_0 conda-forge
gfortran_impl_linux-64 12.1.0 h1db8e46_17 conda-forge
ghostscript 9.18 1 bioconda
giflib 5.2.1 h5eee18b_3
glib 2.78.1 hfc55251_0 conda-forge
glib-tools 2.78.1 hfc55251_0 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.3.0 h59595ed_0 conda-forge
gobject-introspection 1.72.0 py310hbb6d50b_2
graphite2 1.3.13 h58526e2_1001 conda-forge
graphviz 2.50.0 h1b29801_1
gsl 2.7.1 h6e86dc7_1
gtk2 2.24.33 h73c1081_2
gts 0.7.6 hb67d8dd_3
gxx_impl_linux-64 12.1.0 hea43390_17 conda-forge
harfbuzz 5.3.0 h418a68e_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
imagemagick 7.1.0_27 pl5321hae5efcc_0 conda-forge
importlib-metadata 4.11.3 py310h06a4308_0
importlib_metadata 4.11.3 hd3eb1b0_0
jbig 2.1 hdba287a_0
jpeg 9e h5eee18b_1
jq 1.5 0 bioconda
kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h08a2579_0 conda-forge
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libcurl 7.86.0 h2283fc2_1 conda-forge
libdeflate 1.14 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 7.2.0 h69d50b8_2
libgcc-devel_linux-64 12.1.0 h1ec3361_17 conda-forge
libgcc-ng 13.2.0 h807b86a_3 conda-forge
libgd 2.3.3 h6a678d5_3
libgfortran-ng 13.2.0 h69a702a_3 conda-forge
libgfortran5 13.2.0 ha4646dd_3 conda-forge
libglib 2.78.1 hebfc3b9_0 conda-forge
libgomp 13.2.0 h807b86a_3 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libjpeg-turbo 2.1.4 h166bdaf_0 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
librsvg 2.54.4 h7abd40a_0 conda-forge
libsanitizer 12.1.0 ha89aaad_17 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-devel_linux-64 12.1.0 h1ec3361_17 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge
libtiff 4.4.0 h82bc61c_5 conda-forge
libtool 2.4.6 h6a678d5_1009
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp 1.2.4 h11a3e52_1
libwebp-base 1.2.4 h5eee18b_1
libxcb 1.15 h0b41bf4_0 conda-forge
libxml2 2.10.3 hca2bb57_4 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
make 4.3 hd18ef5c_1 conda-forge
ncurses 6.4 h6a678d5_0
ninja 1.10.2 h06a4308_5
ninja-base 1.10.2 hd09550d_5
nspr 4.35 h6a678d5_0
nss 3.89.1 h6a678d5_0
openjpeg 2.4.0 h3ad879b_0
openssl 3.2.0 hd590300_1 conda-forge
pandoc 2.12 h06a4308_3
pango 1.50.12 h382ae3d_0 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
perl 5.32.1 0_h5eee18b_perl5
pip 23.3.1 py310h06a4308_0
pixman 0.42.2 h59595ed_0 conda-forge
pkg-config 0.29.2 h1bed415_8
poppler 22.12.0 h381b16e_0
poppler-data 0.4.11 h06a4308_1
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
python 3.10.13 hd12c33a_0_cpython conda-forge
pyyaml 6.0.1 py310h5eee18b_0
r-abind 1.4_5 r40hc72bb7e_1003 conda-forge
r-askpass 1.1 r40hcfec24a_2 conda-forge
r-assertive.base 0.0_9 r40hc72bb7e_0 conda-forge
r-assertive.files 0.0_2 r40hc72bb7e_1003 conda-forge
r-assertive.numbers 0.0_2 r40h6115d3f_1003 conda-forge
r-assertive.properties 0.0_5 r40hc72bb7e_0 conda-forge
r-assertive.types 0.0_3 r40hc72bb7e_1004 conda-forge
r-assertthat 0.2.1 r40hc72bb7e_2 conda-forge
r-backports 1.4.1 r40hcfec24a_0 conda-forge
r-base 4.0.5 hb87df5d_8 conda-forge
r-base64enc 0.1_3 r40hcfec24a_1004 conda-forge
r-beeswarm 0.4.0 r40hcfec24a_1 conda-forge
r-bh 1.78.0_0 r40hc72bb7e_0 conda-forge
r-bitops 1.0_7 r40h06615bd_0 conda-forge
r-brew 1.0_7 r40hc72bb7e_0 conda-forge
r-brio 1.1.3 r40hcfec24a_0 conda-forge
r-bslib 0.4.0 r40hc72bb7e_0 conda-forge
r-cachem 1.0.6 r40hcfec24a_0 conda-forge
r-cairo 1.6_0 r40h06615bd_0 conda-forge
r-callr 3.7.2 r40hc72bb7e_0 conda-forge
r-catools 1.18.2 r40h7525677_0 conda-forge
r-circlize 0.4.15 r40hc72bb7e_0 conda-forge
r-cli 3.4.1 r40h7525677_0 conda-forge
r-clue 0.3_60 r40hcfec24a_0 conda-forge
r-cluster 2.1.3 r40h8da6f51_0 conda-forge
r-codetools 0.2_18 r40hc72bb7e_0 conda-forge
r-collections 0.3.5 r40hcfec24a_0 conda-forge
r-colorspace 2.0_3 r40h06615bd_0 conda-forge
r-combinat 0.0_8 r40hc72bb7e_1003 conda-forge
r-commonmark 1.8.0 r40h06615bd_0 conda-forge
r-cowplot 1.1.1 r40hc72bb7e_0 conda-forge
r-cpp11 0.4.2 r40hc72bb7e_0 conda-forge
r-crayon 1.5.1 r40hc72bb7e_0 conda-forge
r-crosstalk 1.2.0 r40hc72bb7e_0 conda-forge
r-curl 4.3.2 r40hcfec24a_0 conda-forge
r-cyclocomp 1.1.0 r40hc72bb7e_1004 conda-forge
r-data.table 1.14.2 r40hcfec24a_0 conda-forge
r-dbscan 1.1_10 r40h03ef668_0 conda-forge
r-deldir 1.0_6 r40h8da6f51_0 conda-forge
r-dendextend 1.16.0 r40hc72bb7e_0 conda-forge
r-desc 1.4.2 r40hc72bb7e_0 conda-forge
r-diffobj 0.3.5 r40hcfec24a_0 conda-forge
r-digest 0.6.29 r40h03ef668_0 conda-forge
r-doparallel 1.0.17 r40hc72bb7e_0 conda-forge
r-dotcall64 1.0_1 r40h859d828_0 conda-forge
r-doubletfinder 2.0.3 r40_0 paul.martin-2
r-dplyr 1.0.10 r40h7525677_0 conda-forge
r-dqrng 0.3.0 r40h7525677_0 conda-forge
r-ellipsis 0.3.2 r40hcfec24a_0 conda-forge
r-enrichr 3.1 r40hc72bb7e_0 conda-forge
r-evaluate 0.16 r40hc72bb7e_0 conda-forge
r-fansi 1.0.3 r40h06615bd_0 conda-forge
r-farver 2.1.1 r40h7525677_0 conda-forge
r-fastmap 1.1.0 r40h03ef668_0 conda-forge
r-fields 14.1 r40h8da6f51_0 conda-forge
r-filelock 1.0.2 r40hcfec24a_1002 conda-forge
r-fitdistrplus 1.1_8 r40hc72bb7e_0 conda-forge
r-fnn 1.1.3.1 r40h7525677_0 conda-forge
r-fontawesome 0.3.0 r40hc72bb7e_0 conda-forge
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r-fs 1.5.2 r40h7525677_1 conda-forge
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r-futile.options 1.0.1 r40hc72bb7e_1002 conda-forge
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r-ggplot2 3.3.6 r40hc72bb7e_0 conda-forge
r-ggrastr 1.0.1 r40hc72bb7e_0 conda-forge
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r-globaloptions 0.1.2 r40ha770c72_0 conda-forge
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r-goftest 1.2_3 r40h06615bd_0 conda-forge
r-gplots 3.1.3 r40hc72bb7e_0 conda-forge
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r-gridgraphics 0.5_1 r40hc72bb7e_0 conda-forge
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r-highr 0.9 r40hc72bb7e_0 conda-forge
r-hms 1.1.2 r40hc72bb7e_0 conda-forge
r-htmltools 0.5.3 r40h7525677_0 conda-forge
r-htmlwidgets 1.5.4 r40hc72bb7e_0 conda-forge
r-httpuv 1.6.6 r40h7525677_0 conda-forge
r-httr 1.4.4 r40hc72bb7e_0 conda-forge
r-ica 1.0_3 r40hc72bb7e_0 conda-forge
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r-lifecycle 1.0.2 r40hc72bb7e_0 conda-forge
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r-parallelly 1.32.1 r40hc72bb7e_0 conda-forge
r-patchwork 1.1.2 r40hc72bb7e_0 conda-forge
r-pbapply 1.5_0 r40hc72bb7e_0 conda-forge
r-pheatmap 1.0.12 r40hc72bb7e_2 conda-forge
r-pillar 1.8.1 r40hc72bb7e_0 conda-forge
r-pkgbuild 1.3.1 r40hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r40hc72bb7e_1 conda-forge
r-pkgload 1.3.0 r40hc72bb7e_0 conda-forge
r-plotly 4.10.0 r40hc72bb7e_0 conda-forge
r-plyr 1.8.7 r40h7525677_0 conda-forge
r-png 0.1_7 r40hcfec24a_1004 conda-forge
r-polyclip 1.10_0 r40h7525677_2 conda-forge
r-praise 1.0.0 r40hc72bb7e_1005 conda-forge
r-prettyunits 1.1.1 r40hc72bb7e_1 conda-forge
r-proc 1.18.0 r40h03ef668_0 conda-forge
r-processx 3.7.0 r40h06615bd_0 conda-forge
r-progress 1.2.2 r40hc72bb7e_2 conda-forge
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r-ps 1.7.1 r40h06615bd_0 conda-forge
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r-r.utils 2.12.0 r40hc72bb7e_0 conda-forge
r-r6 2.5.1 r40hc72bb7e_0 conda-forge
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r-rjson 0.2.21 r40h7525677_1 conda-forge
r-rlang 1.0.6 r40h7525677_0 conda-forge
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r-rocr 1.0_11 r40hc72bb7e_1 conda-forge
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r-rpart 4.1.16 r40hcfec24a_0 conda-forge
r-rprojroot 2.0.3 r40hc72bb7e_0 conda-forge
r-rspectra 0.16_1 r40h9f5de39_0 conda-forge
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r-rsvd 1.0.5 r40hc72bb7e_0 conda-forge
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r-sp 1.5_0 r40h06615bd_0 conda-forge
r-spam 2.9_1 r40hb361e29_0 conda-forge
r-spatstat 1.64_1 r40h0357c0b_0 conda-forge
r-spatstat.core 2.4_4 r40h7525677_0 conda-forge
r-spatstat.data 2.2_0 r40hc72bb7e_0 conda-forge
r-spatstat.geom 2.4_0 r40h06615bd_0 conda-forge
r-spatstat.linnet 2.3_2 r40hcfec24a_0 conda-forge
r-spatstat.random 2.2_0 r40h7525677_0 conda-forge
r-spatstat.sparse 2.1_1 r40h06615bd_0 conda-forge
r-spatstat.utils 2.3_1 r40h06615bd_0 conda-forge
r-statmod 1.4.37 r40hc3ea6d6_0 conda-forge
r-stringdist 0.9.8 r40hcfec24a_1 conda-forge
r-stringi 1.7.8 r40h30a9eb7_0 conda-forge
r-stringr 1.4.1 r40hc72bb7e_0 conda-forge
r-styler 1.7.0 r40hc72bb7e_0 conda-forge
r-survival 3.4_0 r40h06615bd_0 conda-forge
r-sys 3.4 r40hcfec24a_0 conda-forge
r-systemfonts 1.0.4 r40hef9c87a_0 conda-forge
r-tensor 1.5 r40hc72bb7e_1003 conda-forge
r-testthat 3.1.4 r40h7525677_0 conda-forge
r-textshaping 0.3.6 r40h9354b80_2 conda-forge
r-tibble 3.1.8 r40h06615bd_0 conda-forge
r-tidyr 1.2.1 r40h7525677_0 conda-forge
r-tidyselect 1.1.2 r40hc72bb7e_0 conda-forge
r-tinytex 0.42 r40hc72bb7e_0 conda-forge
r-utf8 1.2.2 r40hcfec24a_0 conda-forge
r-uwot 0.1.14 r40h7525677_0 conda-forge
r-vctrs 0.4.1 r40h7525677_0 conda-forge
r-vipor 0.4.5 r40hc72bb7e_1003 conda-forge
r-viridis 0.6.2 r40hc72bb7e_0 conda-forge
r-viridislite 0.4.1 r40hc72bb7e_0 conda-forge
r-waldo 0.4.0 r40hc72bb7e_0 conda-forge
r-withr 2.5.0 r40hc72bb7e_0 conda-forge
r-writexls 6.4.0 r40hc72bb7e_0 conda-forge
r-xfun 0.33 r40h7525677_0 conda-forge
r-xml2 1.3.3 r40h7525677_1 conda-forge
r-xmlparsedata 1.0.5 r40hc72bb7e_0 conda-forge
r-xtable 1.8_4 r40hc72bb7e_3 conda-forge
r-yaml 2.3.5 r40h06615bd_0 conda-forge
r-zoo 1.8_11 r40h06615bd_0 conda-forge
readline 8.2 h5eee18b_0
sed 4.8 he412f7d_0 conda-forge
setuptools 68.0.0 py310h06a4308_0
sqlite 3.41.2 h5eee18b_0
sysroot_linux-64 2.12 he073ed8_16 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h0c5db8f_5 conda-forge
toml 0.10.2 pyhd3eb1b0_0
tzdata 2023c h04d1e81_0
wheel 0.41.2 py310h06a4308_0
xmltodict 0.13.0 py310h06a4308_0
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.4.2 h5eee18b_0
yaml 0.2.5 h7b6447c_0
yq 2.12.0 pyhd3eb1b0_0
zipp 3.11.0 py310h06a4308_0
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Hi @zijunmeng, thanks for using our tool. It looks like this is a broader issue with Bioconda and the GenomeInfoDbData package. For now, you can try earlier versions. I was able to get this to work:
conda create --name celda python=3.8
conda activate celda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install bioconductor-celda=1.14.0