saezlab/OmnipathR

loading package failed

Kiliankleemann opened this issue · 1 comments

Kiliankleemann commented

Error: package or namespace load failed for ‘OmnipathR’:
.onLoad failed in loadNamespace() for 'OmnipathR', details:
call: map2(., names(.), function(val, key) {
error: ℹ In index: 1.
ℹ With name: omnipath.url.
Caused by error in str_to_upper():
! lazy-load database '/home/kilian/R/x86_64-pc-linux-gnu-library/4.3/stringi/R/stringi.rdb' is corrupt
In addition: Warning messages:
1: In str_to_upper(.) : restarting interrupted promise evaluation
2: In str_to_upper(.) : internal error -3 in R_decompress1

Package Version

1 abind 1.4-5
2 annotate 1.80.0
3 AnnotationDbi 1.64.1
4 AnnotationHub 3.10.0
5 ape 5.7-1
6 aplot 0.2.2
7 askpass 1.2.0
8 backports 1.4.1
9 base64enc 0.1-3
10 basilisk 1.13.4
11 basilisk.utils 1.13.3
12 beachmat 2.18.0
13 beeswarm 0.4.0
14 BH 1.81.0-1
15 Biobase 2.62.0
16 BiocFileCache 2.10.1
17 BiocGenerics 0.48.1
18 BiocManager 1.30.22
19 BiocNeighbors 1.20.0
20 BiocParallel 1.36.0
21 BiocSingular 1.18.0
22 BiocVersion 3.18.0
23 biomaRt 2.58.0
24 Biostrings 2.70.1
25 bit 4.0.5
26 bit64 4.0.5
27 bitops 1.0-7
28 blob 1.2.4
29 bluster 1.12.0
30 brew 1.0-8
31 brio 1.1.3
32 broom 1.0.5
33 bslib 0.5.1
34 cachem 1.0.8
35 Cairo 1.6-1
36 callr 3.7.3
37 car 3.1-2
38 carData 3.0-5
39 cellranger 1.1.0
40 checkmate 2.3.0
41 circlize 0.4.15
42 cli 3.6.1
43 clipr 0.8.0
44 clue 0.3-65
45 clusterProfiler 4.10.0
46 colorspace 2.1-0
47 commonmark 1.9.0
48 ComplexHeatmap 2.18.0
49 conflicted 1.2.0
50 corrplot 0.92
51 cowplot 1.1.1
52 cpp11 0.4.6
53 crayon 1.5.2
54 credentials 2.0.1
55 crosstalk 1.2.0
56 curl 5.1.0
57 data.table 1.14.8
58 DBI 1.1.3
59 dbplyr 2.4.0
60 DelayedArray 0.28.0
61 DelayedMatrixStats 1.24.0
62 desc 1.4.2
63 DESeq2 1.42.0
64 devtools 2.4.5
65 diffobj 0.3.5
66 digest 0.6.33
67 dir.expiry 1.10.0
68 doParallel 1.0.17
69 DOSE 3.28.0
70 dotCall64 1.1-0
71 downlit 0.4.3
72 downloader 0.4
73 dplyr 1.1.3
74 dqrng 0.3.1
75 DT 0.30
76 dtplyr 1.3.1
77 edgeR 4.0.1
78 ellipsis 0.3.2
79 enrichplot 1.22.0
80 evaluate 0.23
81 fansi 1.0.5
82 farver 2.1.1
83 fastmap 1.1.1
84 fastmatch 1.1-4
85 fgsea 1.28.0
86 filelock 1.0.2
87 FNN 1.1.3.2
88 fontawesome 0.5.2
89 forcats 1.0.0
90 foreach 1.5.2
91 formatR 1.14
92 fs 1.6.3
93 futile.logger 1.4.3
94 futile.options 1.0.1
95 future 1.33.0
96 future.apply 1.11.0
97 gargle 1.5.2
98 genefilter 1.84.0
99 generics 0.1.3
100 GenomeInfoDb 1.38.1

ℹ 251 more rows

ℹ Use print(n = ...) to see more rows

print(n=400, tibble::tibble(

  • Package = names(installed.packages()[,3]),
  • Version = unname(installed.packages()[,3])
  • ))

A tibble: 351 × 2

Package                Version   
<chr>                  <chr>

1 abind 1.4-5
2 annotate 1.80.0
3 AnnotationDbi 1.64.1
4 AnnotationHub 3.10.0
5 ape 5.7-1
6 aplot 0.2.2
7 askpass 1.2.0
8 backports 1.4.1
9 base64enc 0.1-3
10 basilisk 1.13.4
11 basilisk.utils 1.13.3
12 beachmat 2.18.0
13 beeswarm 0.4.0
14 BH 1.81.0-1
15 Biobase 2.62.0
16 BiocFileCache 2.10.1
17 BiocGenerics 0.48.1
18 BiocManager 1.30.22
19 BiocNeighbors 1.20.0
20 BiocParallel 1.36.0
21 BiocSingular 1.18.0
22 BiocVersion 3.18.0
23 biomaRt 2.58.0
24 Biostrings 2.70.1
25 bit 4.0.5
26 bit64 4.0.5
27 bitops 1.0-7
28 blob 1.2.4
29 bluster 1.12.0
30 brew 1.0-8
31 brio 1.1.3
32 broom 1.0.5
33 bslib 0.5.1
34 cachem 1.0.8
35 Cairo 1.6-1
36 callr 3.7.3
37 car 3.1-2
38 carData 3.0-5
39 cellranger 1.1.0
40 checkmate 2.3.0
41 circlize 0.4.15
42 cli 3.6.1
43 clipr 0.8.0
44 clue 0.3-65
45 clusterProfiler 4.10.0
46 colorspace 2.1-0
47 commonmark 1.9.0
48 ComplexHeatmap 2.18.0
49 conflicted 1.2.0
50 corrplot 0.92
51 cowplot 1.1.1
52 cpp11 0.4.6
53 crayon 1.5.2
54 credentials 2.0.1
55 crosstalk 1.2.0
56 curl 5.1.0
57 data.table 1.14.8
58 DBI 1.1.3
59 dbplyr 2.4.0
60 DelayedArray 0.28.0
61 DelayedMatrixStats 1.24.0
62 desc 1.4.2
63 DESeq2 1.42.0
64 devtools 2.4.5
65 diffobj 0.3.5
66 digest 0.6.33
67 dir.expiry 1.10.0
68 doParallel 1.0.17
69 DOSE 3.28.0
70 dotCall64 1.1-0
71 downlit 0.4.3
72 downloader 0.4
73 dplyr 1.1.3
74 dqrng 0.3.1
75 DT 0.30
76 dtplyr 1.3.1
77 edgeR 4.0.1
78 ellipsis 0.3.2
79 enrichplot 1.22.0
80 evaluate 0.23
81 fansi 1.0.5
82 farver 2.1.1
83 fastmap 1.1.1
84 fastmatch 1.1-4
85 fgsea 1.28.0
86 filelock 1.0.2
87 FNN 1.1.3.2
88 fontawesome 0.5.2
89 forcats 1.0.0
90 foreach 1.5.2
91 formatR 1.14
92 fs 1.6.3
93 futile.logger 1.4.3
94 futile.options 1.0.1
95 future 1.33.0
96 future.apply 1.11.0
97 gargle 1.5.2
98 genefilter 1.84.0
99 generics 0.1.3
100 GenomeInfoDb 1.38.1
101 GenomeInfoDbData 1.2.11
102 GenomicRanges 1.54.1
103 gert 2.0.0
104 GetoptLong 1.0.5
105 ggbeeswarm 0.7.2
106 ggforce 0.4.1
107 ggfun 0.1.3
108 ggnewscale 0.4.9
109 ggplot2 3.4.4
110 ggplotify 0.1.2
111 ggpp 0.5.5
112 ggpubr 0.6.0
113 ggraph 2.1.0
114 ggrastr 1.0.2
115 ggrepel 0.9.4
116 ggsci 3.0.0
117 ggsignif 0.6.4
118 ggtree 3.10.0
119 gh 1.4.0
120 gitcreds 0.1.2
121 GlobalOptions 0.1.2
122 globals 0.16.2
123 glue 1.6.2
124 GO.db 3.18.0
125 googledrive 2.1.1
126 googlesheets4 1.1.1
127 GOSemSim 2.28.0
128 graphlayouts 1.0.2
129 gridExtra 2.3
130 gridGraphics 0.5-1
131 GseaVis 0.0.9
132 gson 0.1.0
133 gtable 0.3.4
134 haven 2.5.3
135 HDO.db 0.99.1
136 here 1.0.1
137 highr 0.10
138 hms 1.1.3
139 HPO.db 0.99.2
140 htmltools 0.5.7
141 htmlwidgets 1.6.2
142 httpuv 1.6.12
143 httr 1.4.7
144 httr2 0.2.3
145 ids 1.0.1
146 igraph 1.5.1
147 ini 0.3.1
148 interactiveDisplayBase 1.40.0
149 IRanges 2.36.0
150 irlba 2.3.5.1
151 isoband 0.2.7
152 iterators 1.0.14
153 janitor 2.2.0
154 jquerylib 0.1.4
155 jsonlite 1.8.7
156 KEGGREST 1.42.0
157 knitr 1.45
158 labeling 0.4.3
159 lambda.r 1.2.4
160 later 1.3.1
161 lazyeval 0.2.2
162 liana 0.1.13
163 lifecycle 1.0.4
164 limma 3.58.1
165 listenv 0.9.0
166 lme4 1.1-35.1
167 locfit 1.5-9.8
168 logger 0.2.2
169 lubridate 1.9.3
170 magrittr 2.0.3
171 MASS 7.3-60
172 Matrix 1.6-2
173 MatrixGenerics 1.14.0
174 MatrixModels 0.5-3
175 matrixStats 1.1.0
176 memoise 2.0.1
177 metapod 1.10.0
178 mime 0.12
179 miniUI 0.1.1.1
180 minqa 1.2.6
181 modelr 0.1.11
182 MPO.db 0.99.7
183 munsell 0.5.0
184 nloptr 2.0.3
185 numDeriv 2016.8-1.1
186 OmnipathR 3.11.1
187 openssl 2.1.1
188 openxlsx 4.2.5.2
189 org.Hs.eg.db 3.18.0
190 org.Mm.eg.db 3.18.0
191 parallelly 1.36.0
192 patchwork 1.1.3
193 pbkrtest 0.5.2
194 pheatmap 1.0.12
195 pillar 1.9.0
196 pkgbuild 1.4.2
197 pkgconfig 2.0.3
198 pkgdown 2.0.7
199 pkgload 1.3.3
200 plogr 0.2.0
201 plyr 1.8.9
202 png 0.1-8
203 polyclip 1.10-6
204 polynom 1.4-1
205 praise 1.0.0
206 prettyunits 1.2.0
207 processx 3.8.2
208 profvis 0.3.8
209 progress 1.2.2
210 progressr 0.14.0
211 promises 1.2.1
212 ps 1.7.5
213 purrr 1.0.2
214 quantreg 5.97
215 qvalue 2.34.0
216 R6 2.5.1
217 ragg 1.2.6
218 rappdirs 0.3.3
219 rcmdcheck 1.4.0
220 RColorBrewer 1.1-3
221 Rcpp 1.0.11
222 RcppAnnoy 0.0.21
223 RcppArmadillo 0.12.6.6.0
224 RcppEigen 0.3.3.9.4
225 RcppHNSW 0.5.0
226 RcppML 0.3.7
227 RcppProgress 0.4.2
228 RcppTOML 0.2.2
229 RCurl 1.98-1.13
230 readr 2.1.4
231 readxl 1.4.3
232 rematch 2.0.0
233 rematch2 2.1.2
234 remotes 2.4.2.1
235 reprex 2.0.2
236 reshape2 1.4.4
237 reticulate 1.34.0
238 rjson 0.2.21
239 rlang 1.1.2
240 rmarkdown 2.25
241 roxygen2 7.2.3
242 rprojroot 2.0.4
243 RSpectra 0.16-1
244 RSQLite 2.3.3
245 rstatix 0.7.2
246 rstudioapi 0.15.0
247 rsvd 1.0.5
248 Rtsne 0.16
249 rversions 2.1.2
250 rvest 1.0.3
251 S4Arrays 1.2.0
252 S4Vectors 0.40.1
253 sass 0.4.7
254 ScaledMatrix 1.10.0
255 scales 1.2.1
256 scater 1.30.0
257 scatterpie 0.2.1
258 scran 1.30.0
259 scuttle 1.12.0
260 selectr 0.4-2
261 sessioninfo 1.2.2
262 SeuratObject 5.0.0
263 shadowtext 0.1.2
264 shape 1.4.6
265 shiny 1.7.5.1
266 SingleCellExperiment 1.24.0
267 sitmo 2.0.2
268 snakecase 0.11.1
269 snow 0.4-4
270 sourcetools 0.1.7-1
271 sp 2.1-1
272 spam 2.10-0
273 SparseArray 1.2.2
274 SparseM 1.81
275 sparseMatrixStats 1.14.0
276 statmod 1.5.0
277 stringi 1.8.1
278 stringr 1.5.0
279 SummarizedExperiment 1.32.0
280 sva 3.50.0
281 sys 3.4.2
282 systemfonts 1.0.5
283 testthat 3.2.0
284 textshaping 0.3.7
285 tibble 3.2.1
286 tidygraph 1.2.3
287 tidyr 1.3.0
288 tidyselect 1.2.0
289 tidytree 0.4.5
290 tidyverse 2.0.0
291 timechange 0.2.0
292 tinytex 0.48
293 treeio 1.26.0
294 tweenr 2.0.2
295 tximport 1.30.0
296 tzdb 0.4.0
297 umap 0.2.10.0
298 urlchecker 1.0.1
299 usethis 2.2.2
300 utf8 1.2.4
301 uuid 1.1-1
302 uwot 0.1.16
303 vctrs 0.6.4
304 vipor 0.4.5
305 viridis 0.6.4
306 viridisLite 0.4.2
307 vroom 1.6.4
308 waldo 0.5.2
309 whisker 0.4.1
310 withr 2.5.2
311 xfun 0.41
312 XML 3.99-0.15
313 xml2 1.3.5
314 xopen 1.0.0
315 xtable 1.8-4
316 xts 0.13.1
317 XVector 0.42.0
318 yaml 2.3.7
319 yulab.utils 0.1.0
320 zip 2.3.0
321 zlibbioc 1.48.0
322 zoo 1.8-12
323 base 4.3.2
324 boot 1.3-28
325 class 7.3-20
326 cluster 2.1.2
327 codetools 0.2-18
328 compiler 4.3.2
329 datasets 4.3.2
330 foreign 0.8-82
331 graphics 4.3.2
332 grDevices 4.3.2
333 grid 4.3.2
334 KernSmooth 2.23-20
335 lattice 0.20-45
336 MASS 7.3-55
337 Matrix 1.4-0
338 methods 4.3.2
339 mgcv 1.8-39
340 nlme 3.1-155
341 nnet 7.3-17
342 parallel 4.3.2
343 rpart 4.1.16
344 spatial 7.3-15
345 splines 4.3.2
346 stats 4.3.2
347 stats4 4.3.2
348 survival 3.2-13
349 tcltk 4.3.2
350 tools 4.3.2
351 utils 4.3.2

Kiliankleemann commented

Restarting R worked. Please close.

  • 👍1