Thomas Girke
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/eiR |
| git_branch: devel |
| git_last_commit: 09203f6 |
| git_last_commit_date: 2024-04-30 10:31:10 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 623/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| eiR 1.45.0 (landing page) Thomas Girke
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the eiR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/eiR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: eiR |
| Version: 1.45.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:eiR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings eiR_1.45.0.tar.gz |
| StartedAt: 2024-06-10 02:18:16 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 02:23:18 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 301.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: eiR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:eiR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings eiR_1.45.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/eiR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'eiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eiR' version '1.45.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'eiR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'methods' 'ChemmineR'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'BiocGenerics' 'RCurl' 'RUnit'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
insertEmbeddedDescriptors: no visible global function definition for
'postgresqlWriteTable'
insertEmbeddedDescriptorsByCompoundId: no visible global function
definition for 'postgresqlWriteTable'
insertGroupMembers: no visible global function definition for
'postgresqlWriteTable'
Undefined global functions or variables:
postgresqlWriteTable
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/eiR/libs/x64/eiR.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
eiPerformanceTest 2.69 5.19 15.15
eiCluster 2.83 4.76 15.08
eiMakeDb 2.14 4.85 14.60
eiQuery 2.17 4.73 14.10
eiAdd 2.47 4.42 15.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/eiR.Rcheck/00check.log'
for details.
eiR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL eiR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'eiR' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c optimFunctions.cc -o optimFunctions.o g++ -std=gnu++17 -shared -s -static-libgcc -o eiR.dll tmp.def optimFunctions.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-eiR/00new/eiR/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (eiR)
eiR.Rcheck/tests/runTests.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("eiR")
test_main start
Loading required package: RSQLite
[1] "createing db"
/usr/bin/rm: cannot remove 'test_workspace/data/chem.db': Device or resource busy
eiInit tests
default descriptor
loaded 100 compounds
[1] "100 loaded by eiInit"
setting priorities for 4 groups.
fp descriptor
[1] "createing db"
using cluster
[1] 0
[1] "100 loaded by eiInit"
setting priorities for 4 groups.
starting worker for localhost:11751
starting worker for localhost:11751
starting worker for localhost:11751
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
evaluationg results
Type: EXEC
in indexProcessor: 1
[1] "partFilename: test_workspace/parDist.final.part-1"
starting
Loading required package: eiR
Loading required package: ChemmineR
Loading required package: DBI
Loading required package: RSQLite
in reduce
Type: DONE
Type: DONE
Type: DONE
eiMakeDb
starting worker for localhost:11751
[1] "by file name"
found 96 un-embedded descriptors for runId 1
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Loading required package: eiR
Loading required package: ChemmineR
Loading required package: DBI
Loading required package: RSQLite
Regenerating matrix file...
Regenerating matrix file...
found 50 refs
found 10 samples
checking descriptors
[1] "by number"
found 96 un-embedded descriptors for runId 2
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Regenerating matrix file...
Regenerating matrix file...
found 50 refs
found 20 samples
checking descriptors
[1] "by vector"
found 96 un-embedded descriptors for runId 3
Type: EXEC
Type: EXEC
Type: EXEC
Type: EXEC
Regenerating matrix file...
Regenerating matrix file...
Type: DONE
found 50 refs
found 20 samples
checking descriptors
eiQuery
using runId 3
eiQuery test 1
creating annoy index
loading matrix file
done. num items in index: 96
found 2 queries
eiQuery test 2
creating annoy index
loading matrix file
done. num items in index: 96
found 2 queries
eiQuery test 3
creating annoy index
loading matrix file
done. num items in index: 96
found 2 queries
computing embedded distances on test quries
writing top 50000 to file test_workspace/run-50-40/eucsearch.50-40
A connection with
description "test_workspace/run-50-40/eucsearch.50-40"
class "file"
mode "w"
text "text"
opened "opened"
can read "no"
can write "yes"
[1] "getting test query ids"
writing top 50000 to file test_workspace/data/chemical-search.results
A connection with
description "test_workspace/data/chemical-search.results"
class "file"
mode "w"
text "text"
opened "opened"
can read "no"
can write "yes"
average embedding performance: 0.497059982899883
creating annoy index
loading matrix file
done. num items in index: 96
found 20 queries
average indexing performance: 0.719803568651843
using runId 3
eiAdd test1
loaded 2 compounds
[1] "2 loaded by eiInit"
setting priorities for 0 groups.
found 2 un-embedded descriptors for runId 3
Regenerating matrix file...
creating annoy index
loading matrix file
done. num items in index: 98
found 2 queries
query target distance target_ids
1 3540 3540 0.0000000 301
2 3540 650073 0.7848101 268
3 3540 650007 0.7940199 207
4 3540 650028 0.7989950 227
5 3540 650029 0.8048780 228
6 3540 650037 0.8093385 236
7 3540 650040 0.8093842 239
8 3540 650010 0.8098361 210
9 3540 650019 0.8116343 218
10 3540 650026 0.8141176 225
11 3540 650076 0.8169014 271
12 3540 650041 0.8175896 240
13 3540 650023 0.8252427 222
14 3540 650102 0.8280922 296
15 3540 650030 0.8293515 229
16 3540 650103 0.8312958 297
17 3540 650065 0.8312958 260
18 3540 650106 0.8328267 300
19 3540 650012 0.8341463 212
20 3540 650039 0.8356436 238
21 3540 650083 0.8360277 278
22 3540 650044 0.8410714 243
23 3540 650035 0.8412162 234
24 3540 650072 0.8426966 267
25 3540 650006 0.8428571 206
26 3540 650079 0.8440367 274
27 3540 650104 0.8443878 298
28 3540 650071 0.8468468 266
29 3540 650025 0.8486056 224
30 3540 650100 0.8493151 294
31 3540 650015 0.8502415 215
32 3540 650089 0.8502538 283
33 3540 650101 0.8512658 295
34 3540 650008 0.8513011 208
35 3540 650105 0.8515625 299
36 3540 650059 0.8528428 254
37 3540 650069 0.8539326 264
38 3540 650045 0.8548896 244
39 3540 650027 0.8560000 226
40 3540 650068 0.8568507 263
41 3540 650099 0.8573826 293
42 3540 650080 0.8580645 275
43 3540 650021 0.8591885 220
44 3540 5329468 0.8605341 302
45 3540 650095 0.8642384 289
46 3540 650047 0.8666667 246
47 3540 650061 0.8671329 256
48 3540 650078 0.8671329 273
49 3540 650003 0.8672986 203
50 3540 650024 0.8672986 223
51 3540 650098 0.8690808 292
52 3540 650009 0.8691589 209
53 3540 650002 0.8699764 202
54 3540 650042 0.8752941 241
55 3540 650048 0.8763636 247
56 3540 650034 0.8765432 233
57 3540 650082 0.8778626 277
58 3540 650016 0.8787129 216
59 3540 650058 0.8814815 253
60 3540 650091 0.8820000 285
61 3540 650011 0.8862020 211
62 3540 650017 0.8865979 217
63 3540 650001 0.8872549 201
64 3540 650093 0.8876712 287
65 3540 650013 0.8883721 213
66 3540 650067 0.8885587 262
67 3540 650014 0.8902439 214
68 3540 650092 0.8909348 286
69 3540 650085 0.8924915 279
70 3540 650090 0.8926554 284
71 3540 650038 0.8932927 237
72 3540 650074 0.8951256 269
73 3540 650096 0.8967391 290
74 3540 650032 0.8981324 231
75 3540 650031 0.8992806 230
76 3540 650005 0.8997290 205
77 3540 650081 0.9028571 276
78 3540 650022 0.9031477 221
79 3540 650094 0.9037162 288
80 3540 650020 0.9057971 219
81 3540 650033 0.9074074 232
82 3540 650063 0.9084337 258
83 3540 650077 0.9086758 272
84 3540 650097 0.9090909 291
85 3540 650075 0.9100529 270
86 3540 650004 0.9110738 204
87 3540 650070 0.9118852 265
88 3540 650086 0.9139241 280
89 3540 650049 0.9191686 248
90 3540 650054 0.9214502 251
91 3540 650046 0.9229711 245
92 3540 650050 0.9239905 249
93 3540 650036 0.9292035 235
94 3540 650056 0.9386282 252
95 3540 650087 0.9391101 281
96 3540 650088 0.9411765 282
97 3540 650052 0.9681529 250
98 3540 650043 0.9851301 242
99 5329468 5329468 0.0000000 302
100 5329468 650045 0.5728155 244
101 5329468 650101 0.6554878 295
102 5329468 650100 0.6772727 294
103 5329468 650030 0.7006173 229
104 5329468 650012 0.7449210 212
105 5329468 650104 0.7505882 298
106 5329468 650076 0.7510730 271
107 5329468 650040 0.7525773 239
108 5329468 650065 0.7561521 260
109 5329468 650019 0.7634146 218
110 5329468 650010 0.7681564 210
111 5329468 650025 0.7684564 224
112 5329468 650037 0.7692308 236
113 5329468 650099 0.7698541 293
114 5329468 650105 0.7779817 299
115 5329468 650007 0.7783934 207
116 5329468 650047 0.7807309 246
117 5329468 650096 0.7808564 290
118 5329468 650073 0.7810026 268
119 5329468 650008 0.7895652 208
120 5329468 650069 0.7963526 264
121 5329468 650090 0.7978339 284
122 5329468 650026 0.8000000 225
123 5329468 650011 0.8025035 211
124 5329468 650041 0.8113208 240
125 5329468 650015 0.8125937 215
126 5329468 650028 0.8144989 227
127 5329468 650046 0.8156809 245
128 5329468 650038 0.8208556 237
129 5329468 650072 0.8263069 267
130 5329468 650054 0.8284024 251
131 5329468 650039 0.8295255 238
132 5329468 650092 0.8333333 286
133 5329468 650068 0.8375912 263
134 5329468 650082 0.8376963 277
135 5329468 650048 0.8438538 247
136 5329468 650032 0.8460317 231
137 5329468 650009 0.8485640 209
138 5329468 650016 0.8506494 216
139 5329468 650106 0.8535980 300
140 5329468 650003 0.8559671 203
141 5329468 650036 0.8575130 235
142 5329468 650075 0.8590164 270
143 5329468 650081 0.8592593 276
144 5329468 650080 0.8595506 275
145 5329468 650102 0.8604651 296
146 5329468 650085 0.8605016 279
147 5329468 3540 0.8605341 301
148 5329468 650013 0.8653061 213
149 5329468 650033 0.8701299 232
150 5329468 650050 0.8702128 249
151 5329468 650035 0.8713137 234
152 5329468 650049 0.8719008 248
153 5329468 650044 0.8728682 243
154 5329468 650074 0.8731241 269
155 5329468 650014 0.8785942 214
156 5329468 650079 0.8786127 274
157 5329468 650077 0.8790323 272
158 5329468 650027 0.8807947 226
159 5329468 650097 0.8825503 291
160 5329468 650029 0.8832891 228
161 5329468 650071 0.8840580 266
162 5329468 650098 0.8847926 292
163 5329468 650002 0.8857715 202
164 5329468 650006 0.8864266 206
165 5329468 650058 0.8867925 253
166 5329468 650070 0.8886861 265
167 5329468 650004 0.8900763 204
168 5329468 650103 0.8902196 297
169 5329468 650001 0.8919708 201
170 5329468 650067 0.8927614 262
171 5329468 650095 0.8950131 289
172 5329468 650078 0.8956044 273
173 5329468 650022 0.8960499 221
174 5329468 650094 0.8968134 288
175 5329468 650086 0.8978261 280
176 5329468 650059 0.8979058 254
177 5329468 650093 0.9000000 287
178 5329468 650021 0.9011858 220
179 5329468 650089 0.9028926 283
180 5329468 650034 0.9133127 233
181 5329468 650042 0.9140625 241
182 5329468 650056 0.9153094 252
183 5329468 650083 0.9182156 278
184 5329468 650024 0.9182879 223
185 5329468 650061 0.9222520 256
186 5329468 650087 0.9229209 281
187 5329468 650063 0.9272727 258
188 5329468 650091 0.9294118 285
189 5329468 650088 0.9343629 282
190 5329468 650023 0.9347826 222
191 5329468 650017 0.9448819 217
192 5329468 650020 0.9464286 219
193 5329468 650031 0.9508197 230
194 5329468 650052 0.9744898 250
195 5329468 650005 0.9789030 205
196 5329468 650043 1.0000000 242
checking descriptors
eiAdd test2
loaded 5 compounds
[1] "5 loaded by eiInit"
setting priorities for 0 groups.
found 5 un-embedded descriptors for runId 3
Regenerating matrix file...
creating annoy index
loading matrix file
done. num items in index: 103
found 1 queries
query target distance target_ids
1 23625762 23625762 0.0000000 303
2 23625762 650099 0.6684005 293
3 23625762 650100 0.6847826 294
4 23625762 5329468 0.6994633 302
5 23625762 650104 0.7424961 298
6 23625762 650040 0.7432886 239
7 23625762 650012 0.7579425 212
8 23625762 650011 0.7693989 211
9 23625762 650105 0.7717678 299
10 23625762 650076 0.7760116 271
11 23625762 650069 0.7766204 264
12 23625762 650030 0.7793594 229
13 23625762 650019 0.7804107 218
14 23625762 44137675 0.7830065 305
15 23625762 650045 0.7848537 244
16 23625762 650007 0.7890223 207
17 23625762 650015 0.7920000 215
18 23625762 650072 0.7957393 267
19 23625762 5329098 0.7959184 304
20 23625762 650046 0.7970085 245
21 23625762 650065 0.7997076 260
22 23625762 650090 0.8002577 284
23 23625762 650101 0.8033898 295
24 23625762 650028 0.8118669 227
25 23625762 650008 0.8121137 208
26 23625762 650039 0.8125000 238
27 23625762 3012 0.8202765 307
28 23625762 650092 0.8209424 286
29 23625762 650041 0.8213689 240
30 23625762 650082 0.8215190 277
31 23625762 650102 0.8239896 296
32 23625762 650037 0.8264014 236
33 23625762 650003 0.8288160 203
34 23625762 650073 0.8349359 268
35 23625762 650096 0.8351477 290
36 23625762 650048 0.8379686 247
37 23625762 650054 0.8422782 251
38 23625762 650026 0.8428962 225
39 23625762 650004 0.8438228 204
40 23625762 650044 0.8465116 243
41 23625762 650074 0.8479409 269
42 23625762 650033 0.8515112 232
43 23625762 650068 0.8524173 263
44 23625762 650032 0.8531792 231
45 23625762 650010 0.8594507 210
46 23625762 650001 0.8596882 201
47 23625762 650085 0.8597701 279
48 23625762 650075 0.8613744 270
49 23625762 650009 0.8667737 209
50 23625762 650080 0.8708010 275
51 23625762 650025 0.8734403 224
52 23625762 650081 0.8746130 276
53 23625762 650002 0.8753425 202
54 23625762 650029 0.8772504 228
55 23625762 650038 0.8829114 237
56 23625762 650103 0.8845109 297
57 23625762 650067 0.8867347 262
58 23625762 650083 0.8884514 278
59 23625762 650047 0.8892794 246
60 23625762 650021 0.8905405 220
61 23625762 650016 0.8913649 216
62 23625762 3540 0.8943782 301
63 23625762 650094 0.8977778 288
64 23625762 650013 0.8979866 213
65 23625762 650098 0.9033675 292
66 23625762 650077 0.9038718 272
67 23625762 650089 0.9050894 283
68 23625762 650086 0.9065156 280
69 23625762 3544 0.9065744 306
70 23625762 650106 0.9067669 300
71 23625762 650049 0.9114094 248
72 23625762 650071 0.9116766 266
73 23625762 650036 0.9121726 235
74 23625762 650050 0.9125683 249
75 23625762 650079 0.9154930 274
76 23625762 650027 0.9157303 226
77 23625762 650024 0.9168865 223
78 23625762 650035 0.9196850 234
79 23625762 650097 0.9199536 291
80 23625762 650087 0.9228687 281
81 23625762 650091 0.9249106 285
82 23625762 650006 0.9276527 206
83 23625762 650061 0.9276527 256
84 23625762 650014 0.9286957 214
85 23625762 650063 0.9301075 258
86 23625762 650095 0.9331260 289
87 23625762 650059 0.9347826 254
88 23625762 650056 0.9360000 252
89 23625762 650058 0.9372497 253
90 23625762 650093 0.9390935 287
91 23625762 650070 0.9393204 265
92 23625762 650034 0.9397590 233
93 23625762 650042 0.9406452 241
94 23625762 650031 0.9429967 230
95 23625762 650022 0.9442971 221
96 23625762 650017 0.9446203 217
97 23625762 650078 0.9462875 273
98 23625762 650023 0.9556213 222
99 23625762 650020 0.9635417 219
100 23625762 650088 0.9734345 282
101 23625762 650005 0.9823370 205
102 23625762 650052 0.9909228 250
103 23625762 650043 1.0000000 242
checking descriptors
creating annoy index
test_workspace/run-50-40/matrix.50-404010-1
loading matrix file
done. num items in index: 103
[1] "final refined:"
[,1] [,2] [,3] [,4] [,5]
1 1 NA NA NA NA
2 2 NA NA NA NA
3 3 NA NA NA NA
4 4 NA NA NA NA
5 5 NA NA NA NA
6 6 NA NA NA NA
7 7 NA NA NA NA
8 8 NA NA NA NA
9 9 NA NA NA NA
10 10 NA NA NA NA
11 11 82 NA NA NA
12 12 NA NA NA NA
13 13 NA NA NA NA
14 14 NA NA NA NA
15 15 60 NA NA NA
16 16 NA NA NA NA
17 17 NA NA NA NA
18 18 NA NA NA NA
19 19 NA NA NA NA
20 20 NA NA NA NA
21 21 NA NA NA NA
22 22 NA NA NA NA
23 23 NA NA NA NA
24 24 NA NA NA NA
25 25 NA NA NA NA
26 26 NA NA NA NA
27 27 NA NA NA NA
28 28 NA NA NA NA
29 29 NA NA NA NA
30 30 NA NA NA NA
31 31 NA NA NA NA
32 32 NA NA NA NA
33 33 NA NA NA NA
34 34 NA NA NA NA
35 35 NA NA NA NA
36 36 NA NA NA NA
37 37 NA NA NA NA
38 38 NA NA NA NA
39 39 NA NA NA NA
40 40 NA NA NA NA
41 41 NA NA NA NA
42 42 NA NA NA NA
43 43 NA NA NA NA
44 44 NA NA NA NA
45 45 51 NA NA NA
46 46 NA NA NA NA
47 47 NA NA NA NA
48 48 49 NA NA NA
49 49 48 NA NA NA
50 50 NA NA NA NA
51 51 45 NA NA NA
52 52 NA NA NA NA
53 53 NA NA NA NA
54 54 NA NA NA NA
55 55 NA NA NA NA
56 56 NA NA NA NA
57 57 NA NA NA NA
58 58 NA NA NA NA
59 59 NA NA NA NA
60 60 15 NA NA NA
61 61 NA NA NA NA
62 62 NA NA NA NA
63 63 NA NA NA NA
64 64 NA NA NA NA
65 65 75 NA NA NA
66 66 NA NA NA NA
67 67 NA NA NA NA
68 68 16 NA NA NA
69 69 NA NA NA NA
70 70 NA NA NA NA
71 71 NA NA NA NA
72 72 NA NA NA NA
73 73 NA NA NA NA
74 74 NA NA NA NA
75 75 65 NA NA NA
76 76 NA NA NA NA
77 77 NA NA NA NA
78 78 NA NA NA NA
79 79 NA NA NA NA
80 80 NA NA NA NA
81 81 NA NA NA NA
82 82 11 NA NA NA
83 83 NA NA NA NA
84 84 NA NA NA NA
85 85 NA NA NA NA
86 86 NA NA NA NA
87 87 NA NA NA NA
88 88 NA NA NA NA
89 89 NA NA NA NA
90 90 NA NA NA NA
91 91 NA NA NA NA
92 92 NA NA NA NA
93 93 NA NA NA NA
94 94 NA NA NA NA
95 95 NA NA NA NA
96 96 NA NA NA NA
97 97 102 NA NA NA
98 98 NA NA NA NA
99 99 NA NA NA NA
100 100 NA NA NA NA
101 101 NA NA NA NA
102 102 97 NA NA NA
103 103 NA NA NA NA
$`211`
[1] "211" "286"
$`215`
[1] "215" "264"
$`245`
[1] "245" "251"
$`248`
[1] "248" "249"
$`269`
[1] "269" "279"
$`301`
[1] "301" "306"
clustering:
650001 650002 650003 650004 650005 650006 650007 650008
201 202 203 204 205 206 207 208
650009 650010 650011 650012 650013 650014 650015 650016
209 210 211 212 213 214 215 216
650017 650019 650020 650021 650022 650023 650024 650025
217 218 219 220 221 222 223 224
650026 650027 650028 650029 650030 650031 650032 650033
225 226 227 228 229 230 231 232
650034 650035 650036 650037 650038 650039 650040 650041
233 234 235 236 237 238 239 240
650042 650043 650044 650045 650046 650047 650048 650049
241 242 243 244 245 246 247 248
650050 650052 650054 650056 650058 650059 650061 650063
248 250 245 252 253 254 256 258
650065 650067 650068 650069 650070 650071 650072 650073
260 262 263 215 265 266 267 268
650074 650075 650076 650077 650078 650079 650080 650081
269 270 271 272 273 274 275 276
650082 650083 650085 650086 650087 650088 650089 650090
277 278 269 280 281 282 283 284
650091 650092 650093 650094 650095 650096 650097 650098
285 211 287 288 289 290 291 292
650099 650100 650101 650102 650103 650104 650105 650106
293 294 295 296 297 298 299 300
3540 5329468 23625762 5329098 44137675 3544 3012
301 302 303 304 305 301 307
cid size
[1,] 211 2
[2,] 215 2
[3,] 245 2
[4,] 248 2
[5,] 269 2
[6,] 301 2
2 part clustering
creating annoy index
test_workspace/run-50-40/matrix.50-404010-1
loading matrix file
done. num items in index: 103
[1] "final refined:"
[,1] [,2] [,3] [,4] [,5]
1 1 NA NA NA NA
2 2 NA NA NA NA
3 3 NA NA NA NA
4 4 NA NA NA NA
5 5 NA NA NA NA
6 6 NA NA NA NA
7 7 NA NA NA NA
8 8 NA NA NA NA
9 9 NA NA NA NA
10 10 NA NA NA NA
11 11 82 NA NA NA
12 12 NA NA NA NA
13 13 NA NA NA NA
14 14 NA NA NA NA
15 15 60 NA NA NA
16 16 NA NA NA NA
17 17 NA NA NA NA
18 18 NA NA NA NA
19 19 NA NA NA NA
20 20 NA NA NA NA
21 21 NA NA NA NA
22 22 NA NA NA NA
23 23 NA NA NA NA
24 24 NA NA NA NA
25 25 NA NA NA NA
26 26 NA NA NA NA
27 27 NA NA NA NA
28 28 NA NA NA NA
29 29 NA NA NA NA
30 30 NA NA NA NA
31 31 NA NA NA NA
32 32 NA NA NA NA
33 33 NA NA NA NA
34 34 NA NA NA NA
35 35 NA NA NA NA
36 36 NA NA NA NA
37 37 NA NA NA NA
38 38 NA NA NA NA
39 39 NA NA NA NA
40 40 NA NA NA NA
41 41 NA NA NA NA
42 42 NA NA NA NA
43 43 NA NA NA NA
44 44 NA NA NA NA
45 45 51 NA NA NA
46 46 NA NA NA NA
47 47 NA NA NA NA
48 48 49 NA NA NA
49 49 48 NA NA NA
50 50 NA NA NA NA
51 51 45 NA NA NA
52 52 NA NA NA NA
53 53 NA NA NA NA
54 54 NA NA NA NA
55 55 NA NA NA NA
56 56 NA NA NA NA
57 57 NA NA NA NA
58 58 NA NA NA NA
59 59 NA NA NA NA
60 60 15 NA NA NA
61 61 NA NA NA NA
62 62 NA NA NA NA
63 63 NA NA NA NA
64 64 NA NA NA NA
65 65 75 NA NA NA
66 66 NA NA NA NA
67 67 NA NA NA NA
68 68 16 NA NA NA
69 69 NA NA NA NA
70 70 NA NA NA NA
71 71 NA NA NA NA
72 72 NA NA NA NA
73 73 NA NA NA NA
74 74 NA NA NA NA
75 75 65 NA NA NA
76 76 NA NA NA NA
77 77 NA NA NA NA
78 78 NA NA NA NA
79 79 NA NA NA NA
80 80 NA NA NA NA
81 81 NA NA NA NA
82 82 11 NA NA NA
83 83 NA NA NA NA
84 84 NA NA NA NA
85 85 NA NA NA NA
86 86 NA NA NA NA
87 87 NA NA NA NA
88 88 NA NA NA NA
89 89 NA NA NA NA
90 90 NA NA NA NA
91 91 NA NA NA NA
92 92 NA NA NA NA
93 93 NA NA NA NA
94 94 NA NA NA NA
95 95 NA NA NA NA
96 96 NA NA NA NA
97 97 102 NA NA NA
98 98 NA NA NA NA
99 99 NA NA NA NA
100 100 NA NA NA NA
101 101 NA NA NA NA
102 102 97 NA NA NA
103 103 NA NA NA NA
clustering:
201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
241 242 243 244 245 246 247 248 249 250 251 252 253 254 256 258 260 262 263 264
41 42 43 44 45 46 47 48 48 49 45 50 51 52 53 54 55 56 57 15
265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284
58 59 60 61 62 63 64 65 66 67 68 69 70 71 62 72 73 74 75 76
285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304
77 11 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95
305 306 307
96 92 97
cid size
[1,] 11 2
[2,] 15 2
[3,] 45 2
[4,] 48 2
[5,] 62 2
[6,] 92 2
subset clustering
Regenerating matrix file...
creating annoy index
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpuO5rbh/matrix4010-1
loading matrix file
done. num items in index: 66
[1] "final refined:"
[,1] [,2] [,3] [,4] [,5]
1 1 NA NA NA NA
2 2 NA NA NA NA
3 3 NA NA NA NA
4 4 NA NA NA NA
5 5 NA NA NA NA
6 6 NA NA NA NA
7 7 NA NA NA NA
8 8 NA NA NA NA
9 9 NA NA NA NA
10 10 NA NA NA NA
11 11 NA NA NA NA
12 12 NA NA NA NA
13 13 NA NA NA NA
14 14 NA NA NA NA
15 15 NA NA NA NA
16 16 NA NA NA NA
17 17 NA NA NA NA
18 18 NA NA NA NA
19 19 NA NA NA NA
20 20 NA NA NA NA
21 21 NA NA NA NA
22 22 NA NA NA NA
23 23 NA NA NA NA
24 24 NA NA NA NA
25 25 NA NA NA NA
26 26 NA NA NA NA
27 27 NA NA NA NA
28 28 35 NA NA NA
29 29 NA NA NA NA
30 30 NA NA NA NA
31 31 NA NA NA NA
32 32 NA NA NA NA
33 33 NA NA NA NA
34 34 NA NA NA NA
35 35 28 NA NA NA
36 36 NA NA NA NA
37 37 62 NA NA NA
38 38 NA NA NA NA
39 39 NA NA NA NA
40 40 NA NA NA NA
41 41 NA NA NA NA
42 42 NA NA NA NA
43 43 NA NA NA NA
44 44 NA NA NA NA
45 45 NA NA NA NA
46 46 NA NA NA NA
47 47 65 NA NA NA
48 48 NA NA NA NA
49 49 NA NA NA NA
50 50 NA NA NA NA
51 51 NA NA NA NA
52 52 NA NA NA NA
53 53 NA NA NA NA
54 54 NA NA NA NA
55 55 NA NA NA NA
56 56 NA NA NA NA
57 57 NA NA NA NA
58 58 NA NA NA NA
59 59 NA NA NA NA
60 60 NA NA NA NA
61 61 NA NA NA NA
62 62 37 NA NA NA
63 63 NA NA NA NA
64 64 NA NA NA NA
65 65 47 NA NA NA
66 66 NA NA NA NA
$`248`
[1] "248" "249"
$`264`
[1] "264" "215"
$`245`
[1] "245" "251"
cid size
[1,] 248 2
[2,] 264 2
[3,] 245 2
RUNIT TEST PROTOCOL -- Mon Jun 10 02:23:04 2024
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
eiR RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
Warning messages:
1: In dir.create(test_dir) : 'test_workspace' already exists
2: call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
18.01 5.81 83.17
eiR.Rcheck/eiR-Ex.timings
| name | user | system | elapsed | |
| addTransform | 0 | 0 | 0 | |
| eiAdd | 2.47 | 4.42 | 15.26 | |
| eiCluster | 2.83 | 4.76 | 15.08 | |
| eiInit | 0.62 | 0.25 | 1.17 | |
| eiMakeDb | 2.14 | 4.85 | 14.60 | |
| eiPerformanceTest | 2.69 | 5.19 | 15.15 | |
| eiQuery | 2.17 | 4.73 | 14.10 | |
| freeLSHData | 0 | 0 | 0 | |
| loadLSHData | 0 | 0 | 0 | |
| setDefaultDistance | 0 | 0 | 0 | |