Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-28 11:37:39 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 637/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eiR 1.43.0  (landing page)
Thomas Girke
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/eiR
git_branch: devel
git_last_commit: 78c82dd
git_last_commit_date: 2023-10-24 09:53:29 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for eiR on palomino3


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.

raw results


Summary

Package: eiR
Version: 1.43.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:eiR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings eiR_1.43.0.tar.gz
StartedAt: 2024-03-28 01:42:14 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 01:46:25 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 251.1 seconds
RetCode: 0
Status:   OK  
CheckDir: eiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:eiR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings eiR_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/eiR.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 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 '1.43.0'
* 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-3.19-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 3.20   4.93   17.33
eiCluster         3.02   5.05   17.95
eiAdd             2.64   4.78   20.41
eiQuery           2.30   5.01   17.42
eiMakeDb          1.97   4.93   18.59
* 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-3.19-bioc/meat/eiR.Rcheck/00check.log'
for details.


Installation output

eiR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL eiR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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-3.19-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-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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)

Tests output

eiR.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
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:11181 
starting worker for localhost:11181 
starting worker for localhost:11181 
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:11181 
[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-3.19-bioc\tmpdir\RtmpULbkFJ/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 -- Thu Mar 28 01:46:15 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 
  19.84    3.57   82.06 

Example timings

eiR.Rcheck/eiR-Ex.timings

nameusersystemelapsed
addTransform000
eiAdd 2.64 4.7820.41
eiCluster 3.02 5.0517.95
eiInit0.560.271.42
eiMakeDb 1.97 4.9318.59
eiPerformanceTest 3.20 4.9317.33
eiQuery 2.30 5.0117.42
freeLSHData000
loadLSHData000
setDefaultDistance000